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Aquatic Surveys and Assessment
of the Slim Buttes Region of
Harding and Butte Co., SD

Prepared for:
The Montana and South Dakota TNC Field Offices

By:

David M. Stagliano

Montana Natural Heritage Program

Natural Resource Information System

Montana State Library

October 2006

MONTANA

^ Natural Heritage
Program

Aquatic Surveys and Assessment
of the Slim Buttes Region of
Harding and Butte Co., SD

Prepared for:
The Montana and South Dakota TNC Field Offices

Agreement Number:
1410258002-0000

^^ Library

By:

David M. Stagliano
Aquatic Ecologist

MONTANA

Natural Heritage
Ptt^jtam

y/^^A MONTANA

IlikM Natural Resource

^^W Information System

P.O. Box 201800 #1515 East Sixth Avenue • Helena, MT 59620-1800 • 406-444-5354

This document should be cited as follows:

Stagliano, David M. 2006. Aquatic Surveys and Assessment of the Slim Buttes Region of Harding and
Butte Co., SD. Report to the MT and SD TNC Field Offices. Montana Natural Heritage Program,
Helena, Montana. 59 pp. plus appendices.

Executive Summary

Project goals of the Aquatic Survey and
Assessment of the Slim Buttes Region include: 1)
to sample and assess aquatic community integrity
based on macroinvertebrate, fish and habitat
sampling, 2) to identify and interpret key
community indicators found at the sites, using
standardized protocols and biotic thresholds, and
compare these against reference condition
standards at the watershed-level and local-reach
scale.

Riparian habitat assessments, water quality
parameter measurements, and fish and
macroinvertebrate surveys were performed at 16
lotic (stream) sites and 2 lentic (ponded) sites
within the Slim Buttes Region of the Little Missouri,
Upper South Fork Grand and Upper Moreau
watersheds. Seventeen of these sites had fish, and
all had macroinvertebrates. Two other visited sites
were dry. Three longitudinal sequence stream sites
were sampled in the Little Missouri and South
Moreau rivers; while 2 sequential sites were visited
in the North Fork Moreau, South Fork Grand and
Jones Creek basins. Biological community integrity
was calculated at all sites using Fish Integrated
Biotic Indices (IBI's) and Observed/Expected
Models (O/E), as well as macroinvertebrate multi-
metrics (MT MMI). Site summary descriptions
based on the overall community integrity and site
observations are included.

Site #3 near Hoover showed moderate
improvement in habitat integrity from upstream
sites, but the water quality parameters showed
impairment. The water quality parameters
conductivity and turbidity consistently increased at
the downstream reaches of a stream series.

Fish Communities. Overall, 22 fish species (16
native/6 introduced or exotic) from 6,227 individuals
were reported from all visited sites. Average fish
species richness per site was 8, and the most
diverse sites were the 3 reaches of the Little
Missouri River, with 14 species (11 natives).
Fathead minnows were collected at 16 of 17 (94%)
fish presence sites. The next highest frequency of
occurrence (FO) is the introduced green sunfish at
10 of 17 sites, and the sand shiner and black
bullhead at 9 of 17 sites. Using Montana's Prairie
Fish IBI, 6 of the 17 fish sites were ranked non-
impaired (good to excellent biological integrity), 6
were slightly impaired (moderate integrity) and 5
were moderately impaired (poor biotic integrity).
No sites were ranked severely impaired by the Fish
IBI. The O/E scores agreed with the IBI scores in
most cases, except for the smaller Prairie
Intermittent Streams; the O/E ranked Campbell,
North Fork Moreau #1 and Crooked Creek as
unimpaired (0/E=83.3), while the IBI ranked them
as slightly to moderately impaired (IBI=62, 52 and
49, respectively).

Habitat Evaluations. Highest site habitat scores
using both the EPA RBP (200 max. score) and
BLM (24 max. score) habitat assessment methods
were measured in the South Fork Grand River
basin. South Fork Grand River sites #1 & 2 had
reference site conditions for a Great Plains Prairie
Stream with EPA RBP scores of 188 and 189,
respectively. Most stream sites visited in the Grand
River basin had higher than average landscape
integrity measured at the local reach scale. Two of
the 3 sites in the Little Missouri River basin ranked
excellent for a Medium-Large Prairie River. The
North Fork Moreau River site #2 had the highest
integrity of sites visited in the Moreau River basin.
Sites in the South Fork Moreau River scored
lowest in habitat integrity. The South Fork Moreau

Macroinvertebrate Communities. Overall, 118
macroinvertebrate taxa were reported from the
Slim Butte 2006 assessment sites. Average
macroinvertebrate taxa richness per site was 29
and the highest taxa richness reported at 2 sites
was 50 taxa. Using the Montana DEQ
macroinvertebrate multimetric index (MMI), 9 of
the 18 sites were ranked non- impaired (good to
excellent biological integrity), 6 were slightly
impaired and 3 were moderately impaired. South
Fork Grand River sites #1 & #2 had reference
condition macroinvertebrate scores for a Great
Plains Prairie Stream with DEQ MMI scores of
75.7 and 69.8, respectively. Most stream sites that
contained riffle areas scored much higher with the
MMI than sites with exclusively pool areas. Sites

visited in the South Fork Grand River basin
received higher macroinvertebrate scores than
those in the Moreau basin. The 3 sites in the Little
Missouri River basin that ranked high for fish as a
Medium-Large Prairie River also received
excellent macroinvertebrate integrity scores.

Dragonflies and Damselflies. Incidental
dragonfly and damselfly observations were made
and recorded during the fish and macroinvertebrate
surveys. Three dragonfly species were common
across most sites (Common Green Darner, Anax
Junius', Eight-spotted Skimmer Libellula forensis
and the Variegated Meadowhawk, Sympetrium
corruptum) and no species of concern were noted
at any sites. The pale snaketail, Ophiogomphus
severus, was only spotted at Medium Prairie River
sites with good flow and gravel substrates. The
damselflies (Familiar Bluet, Enallagma civile,
Northern Bluet, Enallagma cyathigerum; Eastern
Forktail, Ischnura verticalis and the Common
Spreadwing, Lestes disjunctus) were common
among the sites. Sites with abundant aquatic
vegetation (South Fork Moreau #1, North Fork
Moreau #1, Crooked Creek, Campbell Creek and
Jones Creek #1 & 2) had abundant populations of
larval damselflies as well.

Amphibian and Reptile Incidentals. Incidental
herpetofauna observations were made and
recorded in conjunction with the fish and
macroinvertebrate surveys. Three amphibian
species (Woodhouse's Toad, Bufo woodhousii,
Great Plains Toad, Bufo cognatus and the
Northern Leopard Frog, Rana pipiens ) and 2
reptile species (Snapping Turtle, Chelydra
serpentina and Plains Garter Snake, Thamnophis
radix) were recorded during the surveys.

Northern Leopard Frogs had the highest site
occupancy rate at 72%.

Integrative Community Assessment. Overall,
diverse fish and macroinvertebrate communities
with high biological integrity are highly correlated
with good riparian condition and high habitat quality
as ranked by the EPA Habitat Quality Index.
Community results from the habitat, fish and
macroinvertebrate surveys combined to rank the
following sites from highest biological integrity to
lowest within their aquatic ecological classification
codes:

Medium Prairie River (AES BOOS): 1) Little
Missouri Montana site, 2) Little Missouri #2, 3)
Little Missouri@ Camp Crook, 4) South Fork
Moreau #3

Northwestern Great Plains Prairie Stream

(AES COOS): 1) South Fork Grand #2, 2) South
Fork Grand #1,3) North Fork Moreau River #2, 4)
Jones Creek #2, S) Crooked Creek, 6) South Fork
Moreau River #2, 7) Bull Creek

Intermittent Prairie Stream (AES code DOOS):
1) North Fork Moreau #1,2) South Fork Moreau
#1; 3) Campbell Creek, 4) Spur Creek, S) Hay
Creek, 6) Jones Creek #1

Intermittent Fishless Prairie Stream (AES
code EOOS): 1) Pine Spring Creek

Northwestern Great Plains Perennial Spring

(AES code SOOS): 1) Picnic Spring

Jones Creek site #2, near the confluence with the
SouthFork Grand River, has high ecological
potential to recover if hydrologic restoration occurs.

Acknowledgments

We would like to thank The Montana and South
Dakota Field Offices of The Nature Conservancy,
especially Brian Martin (MT) and Bob Paulson
(SD). Field work was assisted by Karen Walker;
report reviewer was Linda Vance and report
formatting was provided by Coburn Currier
(MTNHP).

Table of Contents

Introduction 1

Methods 4

Habitat Assessments 5

Fish Communities 5

Macroinvertebrate Communities 6

Results 9

Habitat Assessment 9

Fish Communities 11

Macroinvertebrate Communities 13

Site Description Summaries 15

Conclusions 57

Literature Cited 58

Appendix A. Raw fish data and IBI metric calculations collected from Slim Buttes Sites.
Appendix B. Macroinvertebrate taxa and abundance for the Medium Prairie River (B005) sites
Appendix C. Significant indicator species of the macroinvertebrate community groups reported for the

Slim Buttes Sites.
Appendix D. Macroinvertebrate community descriptions (SPA-species assemblage).
Appendix E. Fish community descriptions (SPA-species assemblage).

List of Figures

Figure 1 . Picnic Spring in the Cave Hills, a small Northwestern Great Plains Perennial Spring 1

Figure 2. The Little Missouri River at the North Dakota border, a Large Prairie River 1

Figures. Untilled landscapes in North America's Great Plains ecoregions 2

Figure 4. Study Site Locations and Level IV Ecoregions within the NGPS Slim Buttes

Study Area, SD 3

Figure 5. Channel depth measurement as part of the habitat and geomorphic assessments 5

Figure 6. Fish sampling a run by seining with a 20 ft straight seine 5

Figure 7. A western silvery minnow seined in the Little Missouri River before release 5

Figure 8. Multi-habitat macroinvertebrate sampling using EPA protocols 6

Figure 9. Dragonfly observations were made in the stream reach. This is an eight-spotted

skimmer (Libellula forensis) 8

Figure 10. The Little Missouri River site near Albion, MT 16

Figure 11. Little Missouri River (AES B005) Medium Prairie River habitat near Albion, MT 16

Figure 12. Little Missouri River (AES B005) cobble/woody debris near Albion, MT 16

Figure 13. Little Missouri River Site #2 (AES B005) run/pool habitat near Ladner, SD 18

Figure 14. Little Missouri River Site #2 (AES B005) sauger (Sander canadensis) an SOC

inMTbutnotSD 18

Figure 15. Little Missouri River Site #2 (AES B005) goldeyes (Hiodon alosoides) a sensitive

indicator Medium-Large Prairie River fish species 18

Figure 16. Little Missouri River Site #1 (AES B005) run/pool habitat near Camp Crook, SD 20

Figure 17 Little Missouri River Site #1 (AES B005) run/pool habitat looking upstream 20

Figure 18. Little Missouri River Site #1 (AES B005) cottonwood stand on upper terrace 20

Figure 19. South Fork Moreau River #3 (AES B005) pool habitat, looking downstream near

Hoover, SD 22

vii

List of Figures (continued)

Figure 20. South Fork Moreau River #3 (AES BOOS) run/pool habitat, looking upstream

near Hoover, SD 22

Figure 21. South Fork Moreau River #3 (AES BOOS) exposed layer of dense fossils in right bank 22

Figure 22. South Fork Moreau River #3 (AES BOOS) petrified tree stumps on right bank 22

Figure 23. South Fork Grand River #2 (AES COOS) with reference condition landscape and

local-reach overview from bridge 2S

Figure 24. South Fork Grand River #2 (AES COOS) bottom of reach looking upstream 2S

Figure 2S. South Fork Grand River #2 (AES COOS) bottom of reach looking downstream 2S

Figure 26. South Fork Grand River #1 (AES COOS) looking downstream towards county bridge 27

Figure 27. South Fork Grand River #1 (AES COOS) bottom riffle of reach looking upstream 27

Figure 28. South Fork Grand River #1 (AES COOS) top ISOm long pool 27

Figure 29. South Fork Grand River #1 (AES COOS) catfish seined in the top pool 27

Figure 30. North Fork Moreau River (AES COOS) Marty Bridge site not sampled 29

Figure 31. North Fork Moreau River #2 (AES COOS) upper riffle looking downstream 29

Figure 32. North Fork Moreau River #2 (AES COOS) bottom of reach looking upstream 29

Figure 33. Jones Creek #2 (AES COOS) pool upstream from road crossing 32

Figure 34. Jones Creek #2 (AES COOS) pools below the road crossing 32

Figure 3S. Jones Creek #2 (AES COOS) typical green sunfish, an introduced species 32

Figure 36. Jones Creek #2 (AES COOS) riffle downstream from road crossing 32

Figure 37. Crooked Creek (AES COOS) looking upstream near Cox Church 3S

Figure 38. South Fork Moreau River #2 (AES COOS) pool habitat, looking upstream near

Rte.8S bridge 37

Figure 39. South Fork Moreau River #2 (AES COOS) pool habitat, top of reach 37

Figure 40. South Fork Moreau River #2 (AES COOS) pool habitat, cottonwood trees top of reach 37

Figure 41. Bull Creek (AES COOS) a silt- impaired Great Plains stream near Brown Rd 39

Figure 42. North Fork Moreau River # 1 (AES DOOS) pool #3 looking upstream 42

Figure 43. North Fork Moreau River #1 (AES DOOS) pool #2 looking upstream 42

Figure 44. South Fork Moreau River #1 (AES DOOS) vegetative pool habitat, looking from bridge 44

Figure 4S. South Fork Moreau River #1 (AES DOOS) beaver dam pool habitat 44

Figure 46. South Fork Moreau River #1 (AES DOOS) pool habitat looking up 44

Figure 47. Campbell Creek (AES DOOS) pool looking downstream towards Brown's Pond 47

Figure 48. Campbell Creek (AES DOOS) pool looking upstream towards inlet 47

Figure 49. Spur Creek (AES DOOS) a tributary to SF Moreau River looking upstream 49

Figure SO. Spur Creek (AES DOOS) a backed up section behind a culvert 49

Figure SI. Hay Creek (AES DOOS) a tributary to SF Moreau River looking upstream SI

Figure S2. Hay Creek (AES DOOS) aquatic water-plantain (Alisma triviale) SI

Figure S3. Jones Creek #1 (AES DOOS) small remaining pool in reach S3

Figure S4. Jones Creek #1 (AES DOOS) dead snapping turtle found on side of Rte. 8S bridge S3

Figure SS. Pine Spring Creek (AES EOOS) a Great Plains Fishless Intermittent Stream with

moderate landscape integrity and degraded local conditions SS

List of Tables

Table 1. Site descriptions for study sites included in the TNC Slim Buttes surveys 4

Table 2. Fish metrics and classification offish species captured in the Slim Buttes Region (2006) 7

Table 3. Impairment determinations from the MMI and O/E (RIVPACS) models 8

viii

List of Tables (continued)

Table 4. Physical measures, WQ parameters and habitat descriptions for the Slim Butte (SD)

study sites 9

Table 5. Aquatic Ecological System types, occurrences in the database and the biological

community groups associated with the defined aquatic ecological communities 10

Table 6. Fish Species Presence, Frequency of Occurrence (FO) all study sites, and for particular

Aquatic Ecological Systems (AES) included in the TNC Slim Buttes surveys 11

Table 7. Fish and macroinvertebrate species, MT IBI, MT MMI and Observed/Expected (O/E)

scores for the Slim Butte (SD) study sites 12

Table 8. Herpetofauna, Aquatic Plant and Dragonfly /Damselfly Species Observations for sites

of the Slim Buttes Watershed Assessment 14

Introduction

Prairie stream systems throughout North America
have suffered neglect due to a lack of
comprehensive study and understanding (Matthews
and Robison 1988, Dodds et al. 2004). Only
recently have there been efforts to sample and
describe the interactions among the state's prairie
stream aquatic biota, and to relate prairie system
aquatic communities to their landscapes. This
study covers one such undocumented area. South
Dakota's Slim Buttes region. From the smallest
prairie spring (Figure 1) to the Little Missouri River
as it leaves South Dakota a large prairie river
(Figure 2), the Slim Buttes region contains a wide
variety of aquatic ecosystems.

Figure 1. Picnic Spring in the Cave Hills, a small
Northwestern Great Plains perennial spring.

As a whole, the Slim Buttes area is an important
part of a large swath of untilled prairie area in the
Level III Northwestern Great Plains ecoregion
(Omerink 1995) (Figure 3), also known as the
Northern Great Plains Steppe (TNC 1999). Four
Level IV ecoregions are found within the Slim
Buttes area (Figure 4). Because intact watershed
landscapes at the regional scale have been shown
to support aquatic communities with high biological
integrity (Allan et al. 1997), we surmised that the
Slim Buttes region might support some of the most
intact native prairie fish and macroinvertebrate
communities in the state. One fairly recent study in
the Moreau River Basin downstream from our
study area reported 19 species offish (16 native)
(Loomis 1997).

To determine if this were true, we used an aquatic
ecosystem classification approach developed by the
Montana Natural Heritage Program (MTNHP) to
increase the understanding of Montana's aquatic
prairie ecosystems (Stagliano 2005). Ecosystem
classification provides a way to understand the
complexity of ecosystems and creates distinctions
among ecosystem types based on factors that
determine the distribution of ecological processes
and biota (Hawkins and Norris 2000). We
previously classified biological communities (fish
and macro invertebrates) within the Missouri River
Zoogeographic Region with respect to the common
repeatable habitat units within the watersheds that
they occur. The Slim Buttes area is within the
same Level III ecoregion, so we hoped that utilizing
these classifications would validate their regional
applicability while allowing us to predict community
types in the scope of watersheds and aquatic
ecological units.

Figure 2. The Little Missouri River at the North
Dakota border, a large prairie river

Untilled Landscapes in the Ecoregions of the Great Plains

Eco regions

1 -Fescue-Mixed Grass Prairie

2 -Aspen Parkland

3 -Northern Great Plains Steppe
4-Dakotas Mixed -Grass Prairie
5 -Black Hills

5 -Northern Tall grass Prairie
7 -Central Tallgrass Prairie

Central Mixed-Grass Prairie

Central Shortgrass Praine

Osage Plains/Flint Hills Prairie

Southern Shortgrass Praine

Crosstimbers and Southern Tallgrass Prairie

Edwards Plateau

14 -Gulf Coast Prairies and Marshes
15 -Tamaulipan Thorn Scrub

Figure 3. Untilled landscapes in North America 's Great Plains ecoregions.

.F. Grand River

North

Figure 4. Study Site Locations and Level IV Ecoregions within the NGPS Slim Buttes
Study Area, SD. 43 a=Missouri Plateau, 43 d=Forested Buttes, 43e=Sagebrush
Steppe, 43j=Moreau Prairie

Methods

Riparian habitat assessments, water quality
parameters, fish and macroinvertebrate surveys
were performed at 1 6 lotic (stream) sites and 2
lentic (ponded) sites within the Slim Buttes Region
of the Little Missouri, Upper South Fork Grand and
Upper Moreau watersheds (Table 1). Seventeen of
these sites had fish, and all had macroinvertebrates.

Two other visited sites were dry. Three
longitudinal sequence stream sites were sampled in
the Little Missouri and South Moreau Rivers, while
2 sequential sites were visited in the North Fork
Moreau, South Fork Grand River and Jones Creek
basins (Site #1 of any sequence is the furthest
upstream site).

Table 1. Site descriptions for study sites included in the TNC Slim Buttes surveys. AES=Aquatic Ecological
System, HUC=8-digit USGS Hydrologic Unit Code, SSO=Strahler Stream Order

Site

AES
Code

Date
Visited

County

HUG

GPS
Lat*

GPS
Long*

Elevation
(ft)

sso

Crooked Creek

COOS

6/6/2006

Harding

10020006

4S.9067

103.S030

3018

Little MO MT

BOOS

6/S/2006

Carter

10110201

4S.27S7

103.647S

3140

Little MO #1

BOOS

6/S/2006

Harding

10110201

4S.S642

103.9S31

3124

Little MO #2

BOOS

6/S/2006

Harding

10110201

4S.77S7

103.886S

3024

Pine Spring Cr

EOOS

6/S/2006

Harding

10130302

4S.S469

103.7800

3064

S F Grand #1

COOS

6/7/2006

Harding

10130302

4S.6389

103.3128

2721

Jones Cr #2

COOS

6/7/2006

Harding

10130302

4S.6390

103.3232

2730

S F Grand #2

COOS

6/6/2006

Harding

10130302

4S.639S

102.9990

2S81

Jones Cr #1

DOOS

6/6/2006

Harding

10130302

4S.6877

103.488S

300S

Bull Creek

DOOS

6/S/2006

Harding

10130302

4S.7841

103.S007

288S

Campbell Cr

DOOS

6/S/2006

Harding

10130302

4S.8092

103.4997

2934

S F Moreau #3

BOOS

6/7/2006

Butte

10130304

4S.1168

103.2709

27S0

S F Moreau #2

COOS

6/6/2006

Butte

10130304

4S.1261

103.S497

2919

S F Moreau #1

DOOS

6/6/2006

Butte

10130304

4S.178S

103.6S08

2968

Spur Creek

DOOS

6/6/2006

Butte

10130304

4S.188S

103.63S4

2997

Hay Creek

DOOS

6/6/2006

Butte

10130304

4S.1983

103.6238

299S

N F Moreau #2

COOS

6/7/200S

Harding

1013030S

4S.2697

103.1979

2821

Antelope Creek

(old sample site)

Antelope Creek

(dry)

N F Moreau #1

DOOS
DOOS
DOOS

7/8/2000
6/7/200S
6/6/2006

Perkins
Perkins
Harding

1013030S
1013030S
1013030S

4S.3132
4S.3272
4S.3S7S

102.6876
102.9204
103.S479

2822
284S
3071

2
1
2

Rabbit Creek (dry)

DOOS

6/7/200S

Perkins

10130305

4S.4436

102.9110

279S

*GPS readings were

taken from the top and bottom of reach, only top GPS reading i

s reported here.

Habitat Evaluations

On-site habitat assessments were conducted using
the rapid assessment protocol (RBP Level 1,
scores 0-200) developed for the EPA by Barbour et
al. (1999) with modifications and additions by the
National Aquatic Assessment of the Bureau of
Land Management (BLM) Buglab (scores 0-24)
(http://wwwl .usu.edu/buglab/forms/
Bug%20Protocol%20form.pdf). Using the BLM
assessment protocols, the reach was divided into 10
equally spaced transects. Parameters recorded at
each were: wetted width, bankfull width, 3 channel
depth measurements, large woody debris and
riparian shading. Basic water chemistry
parameters (temperature, pH, conductivity,
dissolved O^and turbidity) were recorded prior to
sampling using the Horiba H-10. The goal of these
evaluations is to characterize local reach
geomorphology, riparian and in-stream habitat, and
other characteristics that influence aquatic
community integrity (Figure 5). The sites ranking
higher using these protocols are determined to have
higher quality local-scale habitat. Habitat
assessments were performed during the same visit
as the biological sampling.

Figure 5. Channel depth measurement as part of the
habitat and geomorphic assessments.

Fish Communities

Fish sampling protocols (MTFWP 2003) required
the positioning of upstream and downstream block
nets at the ends of the reach (300m or 40x wetted
width), but most of the time shallow sections and/or
riffle areas were sufficient to prevent fish from

escaping while the run & pool areas were being
seined from the upstream to the downstream
direction with a 20-30 ft Va inch straight seine,
depending on wetted width (Figure 6). Fish were
transferred to holding buckets, identified to species,
enumerated in the field, examined for external
anomalies (e.g. deformities, eroded fins, lesions,
and tumors), and then released (Figure 7). Young-
of-the-year fish less than 20 millimeters in length
were noted on the field sheet (not included in the
totals), and released. Voucher specimens were only
taken in the case of uncertain field identifications of
the silvery minnows, Hybognathus spp., which
were preserved in 10% buffered formalin and
identified in the lab. Vouchers were submitted to
the Montana State University fish collection.

Figure 6. Fish sampling a run by seining with a 20 ft
straight seine.

Figure 7. A western silvery minnow seined in the
Little Missouri River before release.

Analysis of the sampled fish communities used
Integrated Biotic Indices (IBI) (Bramblett et al.
2005) and derived Observed/Expected (O/E) Fish
Models (Stagliano 2005) to detect impairment in the
biological integrity of the sites. The IBI involved
calculation of a series of metrics evaluating
different attributes of the community (Table 2).
The metrics allowed calculation of an overall score
between and 100. Bramblett et al. (2005) did not
propose threshold criteria for good, fair, and poor
biological integrity for these scores. Therefore, we
applied commonly used criteria. Scores of 75 to
1 00 indicate good to excellent biological integrity,
50-74 fair to good biological integrity, 25 to 49
indicated poor to fair biological integrity and scores
<25% indicate poor biological integrity or severely
impaired.

Macroinvertebrate Communities

Macroinvertebrates were collected from all
habitats that we could wade within the sampling
reach of the streams (Figure 8). Sampling involved
multi-habitat, qualitative methods outlined in the
EPA protocols (Barbour et al. 1999). Cobble
substrates, vegetation, woody debris and bank-side
areas were sampled qualitatively with a 500-micron
D-frame net within the designated transects. A
total of twenty habitat-weighted, randomized 0.5m
jabs or kicks were conducted within the reach,
allowing 10 seconds per kick and composited into
one sample. All organisms in the net were washed
on a 500-micron sieve, transferred to a 1 liter
Nalgene bottle, labeled and preserved in 95%

Figure 8. Multi-habitat macroinvertebrate sampling
using EPA protocols.

ethanol and brought to the MTNHP lab in Helena
for processing.

These samples were processed (sorting,
identification, and data analysis) by David Stagliano
at the Helena lab following DEQ protocols (MT
DEQ 2005). Macroinvertebrates were identified to
the lowest taxonomic level, imported into EDAS
(Jessup 2006), and biological metrics were
calculated from the data using the Montana
Department of Environmental Quality's newest
multimetric macroinvertebrate (MMI) protocols
(Jessup et al. 2005, Feldman 2006). Metric results
were then scored using the Montana DEQ
bioassessment criteria and each sample categorized
as non- impaired or impaired according to threshold
values (Table 3).

The macroinvertebrate MMI score is based upon a
series of metrics that measure attributes of benthic
macroinvertebrate communities regarding condition
changes to a stream system (in the form of
pollution or pollutants). The invertebrate metrics
include: EPT Taxa Richness (Score = EPT
richness/14* 100): Ephemeroptera, Plecoptera
&Trichoptera taxa; Percent Tanypodinae (Score
= PercentTanypodinae/10 *100): Percent
Orthocladiinae of Chironomidae (Score =
(100-percent Orthocladiinae of Chironomidae/
100)*100); Predator Taxa Richness (Score =
number of predator taxa/9*100); Percent
Collectors and Filterers (Score = (100 -
percent collectors and filterers/65)*100): This
metric measures the relative abundance of
collector and filterer taxa in the sample. The index
score represents the condition of the
macroinvertebrate community at the time the
sample was collected within that past year. If the
index score is below the impairment threshold, the
individual metrics can be used to provide insight as
to why the communities are different from the
reference condition (Barbour et al. 1999, Jessup et
al. 2005). The impairment threshold set by MT
DEQ is 37 for the Eastern Plains Stream Index;
thus any scores above this threshold are considered
unimpaired. South Dakota does not yet have
macroinvertebrate models to calculate scores. For
the Observed/Expected (O/E) scores, taxa in the
sample were compared to their expected
macroinvertebrate indicator species for that
classified prairie aquatic ecological type (Stagliano
2005) (Appendix C).

Table 2. Fish metrics and classification offish species captured in the Slim Buttes Region (2006).

Species

Scientific Name

Trophi

Feeding

Litho-

Tol**

Origin

Total

Modef

obligate
Reprod
GuildJ

Length
3 years

Hiodontidae

Goldeye

Hiodon alosoides

INT

259

Catostomidae

River carpsucker

Carpiodes carpio

MOD

229

Shorthead Redhorse

Moxostoma
macroledidotum

MOD

254

White sucker

Catostomus commersoni

TOL

229

Cyprinidae

Common carp

Cyprinus carpio

TOL

381

Golden shiner

Notemigonus crysoleucas

MOD

102

Flathead Chub

Platygobio gracilis

MOD

140

Fathead Minnow

Pimephales promelas

TOL

Longnose dace

Rhinichthys cataractae

INT

Brassy minnow

Hybognathus hankinsoni

MOD

Plains minnow

Hybognathus placitus

MOD

Western silvery

Hybognathus argyritis

MOD

minnow

Sand shiner

Notropis stramineus

MOD

Esocidae

Northern pike

Esox lucius

MOD

457

Gasterosteidae

Brook stickleback

Culaea inconstans

TR§

MOD

Centrarchidae

Green sunfish

Lepomis cyanellus

TOL

102

Percidae

Iowa darter

Etheostoma exile

INT

Sanger

Sander canadensis

MOD

279

Ictaluridae

Channel catfish

Ictalurus punctatus

TR§

MOD

254

Stonecat

Noturus flavus

INT

140

Black bullhead

Ameiurus melas

TR§

TOL

152

Yellow bullhead

Ameiurus natalis

TR§

MOD

254

*HB = herbivore (> 90% plants or detritus); IC = invertivore/carnivore (>25% both invertebrates and vertebrates); IN =
invertivore; OM = omnivore(25-90% plants or detritus) CA=carnivore (90% fish or other vertebrates);

t BE = benthic; GE = generalist; WC = water column: Brown (1971); Scott and Crossman (1973); Becker (1983)

{ LO=Litho-obligate Reproductive Guild; Scott and Crossman (1973); Pflieger (1997); Barbour et al. (1999)

§ Tolerant reproductive strategists are not litho-obligates, use parental care at spawning site: Scott and Crossman (1973);

Pflieger (1997)

** INT = intolerant; MOD = moderately tolerant: TOL = tolerant; Barbour et al. (1999);

tt N = native; I - introduced; Holton and Johnson (2003), SD Fish Species List (SD Heritage Program)

Table 3. Impairment determinations from the MMI and
O/E (RIVPACS) models (taken from Jessup et al. 2005,
Feldman 2006).
Ecoregion [RIVPACS |MMI |lmpairment Determination

Mountain

Low Valley

Eastern Plains

>0.8 or<1.2
<0.8 or > 1.2

>0.8 or < 1.2
<0.8 or > 1.2

>63
<63

>48
<48

>37
<37

Not impaired
Impaired

Dragonflies and Damselflies

Incidental dragonfly and damselfly observations
were made and recorded during the fish and
macroinvertebrate surveys. The dragonfly
identifications and observations were usually done
on the wing, but we did collect numerous
damselflies and an occasional reference dragonfly
using an aerial sweep net along the riparian
vegetation (Figure 9).

Figure 9. Dragonfly observations were made in the
stream reach. This is an eight-spotted skimmer
(L ibellula for ens is) .

Results

The Slim Buttes region of northwest South Dakota
is an excellent example of untilled, intact
Northwestern Great Plains or Northern Great
Plains Steppe. The extent of some of these intact
prairies and quality of the landscape rivals or
exceeds landscapes that I have personally seen in
Northwestern Great Plains reference sites of
southeast Montana. One of the most impressive
areas includes the landscape of the South Fork of
the Grand River watershed, which exhibited high
integrity at the landscape level and at the local
stream-reach scale. We identified fish and
macro invertebrate communities with high
ecological integrity within 5 Prairie Aquatic
Ecological Systems (AES) during this study:
Medium Prairie River (AES BOOS), Northwestern
Great Plains Prairie (AES COOS) and Intermittent
Prairie Streams (AES code DOOS), Intermittent
Fishless Prairie Stream (AES code EOOS) and the
Northwestern Great Plains Perennial Spring (AES
code SOOS) (Table 4).

Habitat Evaluations

Overall, 11 of 1 8 sites had good to excellent habitat
quality ranked by at least one of the assessment

methods (Table S). Highest site habitat scores
using both the EPA RBP (200 max. score) and
BLM (24 max. score) habitat assessment methods
were measured in the South Fork Grand River
basin. South Fork Grand River Sites #1 & #2 had
reference site conditions for a Great Plains Prairie
Stream with EPA RBP scores of 188 and 189,
respectively (Table S). Most stream sites visited in
the Grand River basin had higher than average
landscape integrity measured at the local reach-
scale. All sites in the Little Missouri River basin
ranked high for a Medium-Large Prairie River. The
North Fork Moreau River site #2 had the highest
integrity of sites visited in the Moreau basin. Sites
in the South Fork Moreau River scored lowest in
habitat integrity. South Fork Moreau site #3 near
Hoover showed moderate integrity but the water
quality parameters show impairment. The water
quality parameters conductivity and turbidity both
increased at the downstream reaches of a stream
series. Two conductivity values that would exceed
DEQ impairment standards in Montana were
recorded at the South Fork Moreau River #3 and
the Crooked Creek sites (>3,000y4s).

Table 4. Aquatic Ecological System types, biological community groups (SPA) associated with the defined
aquatic ecological communities and occurrences in the Slim Buttes Study Area.

Aquatic Ecological

AES

Fish SPA^

Macroinvert

Number of

System

code

groups*

Occurrence**

Medium Prairie River

BOOS

1,2, 18,20

3,9,11,37,40

Ecosystem

Great Plains Prairie Stream

COOS

2,20

9, 11,12,37

Ecosystem

Great Plains Intermittent

DOOS

18,20

9, 12

Stream Ecosystem

Great Plains Fishless

EOOS

None

Intermittent Stream

Ecosystem

Small Fishless Prairie Spring

SOOS

None

1,12

Ecosystem

^See Appendix E for Fish Species Assemblages

* See Appendix C & D for Macroinvertebrate species groups

**Number of sites visited with data collected

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Fish ContntUniticS ^^ ^^^ Great Plains Intermittent Prairie Streams, the

species occurring most often were the brook

Overall, 22 fish species (16 native/6 introduced or

exotic) from 6,227 individuals were reported from

all visited sites (Table 2, Appendix A). Average

fish species richness per site was 8, and the most ,, i • i • i • • x ^ i- i i

,. .^ ^1 ^ 1 r.^1 T -^1 excellent biologicalmtegrity), 6 were slightly

diverse sites were the 3 reaches of the Little . ... ... .. .

Missouri River, with 14 species (11 natives).

Fathead minnows were collected at 16 of 17 (94%)

fish presence sites. The next highest frequency of

occurrence (FO) is the introduced green sunfish at

10 of 17 sites, and the sand shiner and black

bullhead at 9 of 17 sites. Flathead chubs and plains

minnows round out the top 6 fish species collected

across all fish sites (Table 6). Fish species highly

associated (100% of the time) with the Medium

Prairie River Ecological System (AES BOOS)

included sand shiner, flathead chub, plains minnow,

channel catfish, white sucker, river carpsucker,

stonecat and western silvery minnow (Table 6).

stickleback, brassy minnow and fathead minnow
(Table 6). Using Montana's Prairie Fish IBI, 6 of
the 17 fish sites were ranked non- impaired (good to

impaired (moderate integrity) and 5 moderately
impaired (poor biotic integrity) (Table 7). No sites
were ranked severely impaired by the Fish IBL
The O/E scores agreed with the IBI scores in most
cases, except for the smaller Prairie Intermittent
Streams; the O/E ranked Campbell, North Fork
Moreau #1 and Crooked Creek as unimpaired (O/
E=83.3), while the IBI ranked them as slightly to
moderately impaired (IBI=62, 52 and 49,
respectively).

Fish community structure in the Slim Buttes sites
responded to two primary landscape factors: the

Table 6. Fish Species Presence, Frequency of Occurrence (FO) at all study sites, and for
particular Aquatic Ecological Systems (AES) included in the TNC Slim Buttes surveys.
Blanks indicate absence from that stream type.

Fish Species

# of Sites

Overall

AES

Present

B005

C005

D005

Fatliead Minnow

0.94

0.75

1.00

BlacliBullIiead

0.59

0.50

1.00

0.29

Green Sunfish

0.59

0.75

1.00

0.14

Sand Shiner

0.53

1.00

0.83

Flathead Chub

0.47

1.00

0.67

Plains Minnow

0.47

1.00

0.67

Channel Catfish

0.41

1.00

0.50

Longnose Dace

0.41

0.75

0.67

White Sucker

0.41

1.00

0.33

0.14

River Carpsuclcer

0.35

1.00

0.33

Stonecat

0.35

1.00

0.33

Western Silvery

0.35

0.75

0.50

Minnow

Brook Stickleback

0.18

0.17

0.29

Common Carp

0.18

0.75

Goldeye

0.18

0.75

Shorthead Redhorse

0.18

0.75

Yellow Bullhead

0.12

0.33

Golden Shiner

0.12

0.17

0.14

Iowa Darter

0.12

0.17

0.14

Brassy Minnow

0.06

0.14

Northern Pike

0.06

0.25

Sanger

0.06

0.25

stream size/drainage area & discharge (lotic-
connected vs. lentic-ponded-unconnected
conditions), and the human- factor, stock pond/fish
species introductions. Increasing drainage area
directly relates to increasing fish diversity
(Angermeier and Schlosser 1989, Bramblett et al.
2005), which is evident in the greater number of
expected indicator species in our fish assemblages
for the medium and larger prairie river systems.
Clearly, measures of connectivity are important in
structuring fish communities (Matthews and
Robison 1998, Bramblett and Fausch 1991). Many

fish, even warmwater species (e.g. sauger, channel
catfish), are migratory during their spawning
periods (Holton and Johnson 2003) or pioneering
(e.g. white sucker, shorthead redhorse) and will
opportunistically search for suitable habitats. If the
conditions are favorable for fish species to migrate
into a particular type of aquatic system, especially
if connectivity is complete across the basin or there
is connectivity to reservoirs or other pools of non-
native fishes, then the community observed might
be surprisingly different than what was expected.
This explains white suckers co-occurring with

Table 7. Fish and macroinvertebrate species, IBFs, MT MMFs and Observed/Expected (O/E)
scores for the Slim Butte (SD) study sites. Bold-underlined score are good-excellent reach
scores, shaded gray represent fair-good local-reach conditions.

Fish

O/E

Macro-

O/E

Species

IBI

invert

MMI

Total

Native

Taxa

Moreau River Basin

N F Moreau #1

S131

75TO

28.00

6G.D0

N F Moreau #2

90.26

103.23

57.00

>80

S F Moreau #1

56.65

51.61

35.00

65.00

S F Moreau #2

34.92

38.71

22.00

40.00

S F Moreau #3

71.30

116.13

45.60

62.00

Tribto S.F. Moreau (Spur)

48.08

50.00

34.92

60.00

Tribto S.F.Moreau (Hay)

49.91

50.00

28.00

55.00

Grand River Basin

Jones Cr#1

44.76

50.00

35.60

61.00

Jones Cr#2

88.29

64.52

58.90

>80

S F Grand #1

99.77

116.13

75.70

>80

S F Grand #2

103.61

116.13

69.80

>80

Campbell Creek

62.05

83.30

35.60

>80

BullCr#1

43.60

50.00

24.80

50.00

Crooked Cr #1

51.97

83.30

39.50

>80

Pine Spring Creek

no fish

32.50

61.00

Little Missouri River

Basin

Little MO #2

87.63

100.00

72.60

>80

Little MO #1 Camp Crook

65.19

92.10

63.37

>80

Little MO MT

88.05

100.00

62.50

>80

fathead minnows and brook sticklebacks, the usual
inhabitants, in the upper South Fork Moreau site

#1.

The influence offish stocking is considerable.
Green sunfish and black bullhead, two introduced
fish species, dominated some sites. We know that
most stock ponds and reservoirs in this part of the
state have been stocked with various introduced
species of fish at some time (Doug Backland, SD
NHP, pers. comm. 2006). In addition to reducing
native fish numbers through competition, stocked
fish can often overwhelm a stream reach and
displace the natives. Since the non-native or
stocked fish now represent self-sustaining
communities, they have considerable influence on
the stream ecosystems.

Macroinvertebrate Communities

Overall, 118 macroinvertebrate taxa were reported
from the Slim Butte 2006 assessment sites.
Average macroinvertebrate taxa richness per site
was 29 and the highest taxa richness reported at
one site (Little Missouri) was 50 taxa (Appendix
B). Using the Montana DEQ macroinvertebrate
multimetric index (MMI), 9 of the 18 sites were
ranked non- impaired (good to excellent biological
integrity), 6 were slightly impaired and 3
moderately impaired (Table 7). South Fork Grand
River sites #1 & #2 had reference condition
macroinvertebrate scores for a Great Plains Prairie
Stream with DEQ MMI scores of 75.7 and 69.8,
respectively (Table 7). The Little Missouri River
sites ranked excellent with Montana MMI scores in
the 60's and lower 70's. Sites visited in the South
Fork Grand River basin received higher
macroinvertebrate scores than those in the Moreau
basin. The 3 sites in the Little Missouri River basin
that ranked high for fish as a Medium-Large
Prairie River, received excellent macroinvertebrate
integrity scores. Macroinvertebrate community
structure in the Slim Buttes sites responded to
similar landscape factors as found with fish (stream
size and lotic-connected vs. lentic-ponded-
unconnected conditions), but were less affected by
the connectivity of pools. However, most stream
sites that contained riffle areas between the pools
scored much higher with the MMI than sites with
exclusively pool areas. The Montana MMI was

not as effective at ranking intermittent sites that
contained intact communities, but were dominated
by the more tolerant species of that assemblage.

Dragonflies and Damselflies

Incidental dragonfly and damselfly observations
were made and recorded during the fish and
macroinvertebrate surveys (Table 8). Three
dragonfly species were common across most sites
(Common Green Darner, Anax Junius', Eight-
spotted Skimmer, Libellula forensis and the
Variegated Meadowhawk, Sympetrium
corruptum) and no species of concern were noted
at any sites. The pale snaketail, Ophiogomphus
severus, was only spotted at Medium Prairie River
sites with good flow and gravel substrates. The
damselflies (Familiar Bluet Enallagma civile,
Northern Bluet, Enallagma cyathigerum, Eastern
Forktail, Ischnura verticalis and the Common
Spreadwing, Lestes disjunctus) were common
among the sites. Sites with abundant aquatic
vegetation (South Fork Moreau #1, North Fork
Moreau #1, Crooked Creek, Campbell Creek and
Jones Creek #1 & 2) had abundant populations of
larval damselflies as well.

Amphibian and Reptile Incidentals

Incidental herpetofauna observations were made
and recorded in conjunction with the fish and
macroinvertebrate surveys. Three amphibian
species (Woodhouse's Toad, Bufo woodhousii,
Great Plains Toad, Bufo cognatus and the
Northern Leopard Frog, Rana pipiens ) and 2
reptile species (Snapping Turtle, Chelydra
serpentina and Plains Garter Snake, Thamnophis
radix) were recorded during the surveys.
Northern Leopard Frogs had the highest site
occupancy rate at 72%.

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Site Description Summaries

Medium Prairie River Ecological Types

Medium Prairie River (AES BOOS) Ecological Types in order of highest biological integrity to lowest. 1)
Little Missouri Montana site, 2) Little Missouri #2, 3) Little Missouri® Camp Crook, 4) South Fork
Moreau #3

Management/Threats to this ecological system include: Grazing and livestock use around the
riparian areas occurs and can have strong local effects resulting in sedimentation and stream widening at
cattle crossings. Introductions of game or forage fish in stock ponds anywhere in the watershed can
make their way downstream to these larger prairie rivers and become permanent residents, competing
with (green sunfish) or preying upon (northern pike) resident native fish species

Global Rank Comments: The number of viable occurrences is unknown, but probably somewhat rare.
These prairie river ecological types are abundant in terms of river miles across the Northern Great Plains
Steppe of North America, but the hydrology (i.e. water permanence) and biological integrity can be easily
affected by upstream dams or diversions in the watershed. Stock ponds that are stocked with game fish,
and bait bucket introductions can also contribute to the community degradation of introduced fish species.

Site Description

Little Missouri River (MT site)

LITTLE MISSOURI
RIVER

Figure 10. The Little Missouri River site near Albion,
MT.

Figure 11. Little Missouri River (AES B005) Medium Figure 12. Little Missouri River (AES B005) cobble/
Prairie River habitat near Albion, MT. woody debris near Albion, MT.

Location: Accessed from Stateline Rd. at bridge crossing about 6 miles Northeast of Albion, MT.
Proceeded upstream -100m to the first riffle/pool set designated as the bottom of the reach (Figure 11).

Nearest Town: Albion, Carter County, MT

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: B005-Northwestern Great Plains Medium Prairie Stream, borderline
Large Prairie River probably shifts around the ND border.

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
slight impacts, cattle on right bank.

Rare or Unique Species: No rare species, but giant floater mussel shells were documented.

Rare Features: No rare features documented.

Introduced/Exotic Species: Black bullhead, carp and green sunfish

Overall Ecological Site Condition: Good

Reach Summary: The 300 m reach consisted of 2 riffle/run/pool complexes with full flowing water
connectivity. The lower pool was -50m long (averaged 0.75m deep) and contained the deepest fish
holding habitat. This stream reach has good aquatic habitat and a diversity of microhabitats, thus leading
to high fish species diversity (14 species, 11 native), although an abundance & dominance of introduced
species. Pools averaging 25-40m long and 8- 10m wide. All substrate of the upper pool was gravel/silt
dominated with some cobbles, and pool #2 was dominated by silt & gravel. Aquatic geomorphic
structures and overhanging banks at the margins provided most fish habitat in this stream reach. Riparian
vegetation coverage was dominated by shrubs & some willows on the immediate riparian bank with
cottonwoods along the 2nd tier riparian area. Livestock use index (LUI) was low with only -7 cow pies
counted on a 75m walk of the left and right banks.

Reach Habitat Ranking: BLM= 95.8% (23 of 24) EPA RBP= 94% (188 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-4 with a
gentle-medium slope (-1%)), moderate sinuosity, riffle-pool configuration with substrate dominated by
gravel and sand/silt dominated pools. Pools are slightly incised and averaged >40 cm in depth.. Wetted
width of the reach was 9.8m. Surrounding bank materials are finer than the channel bed materials
indicating no in-stream accumulation of sediments.

Amphibian Community: 1 adult Northern Leopard Frog (NLF) present.

Fish Community: 14 fish species (11 native) were seined in the 2 riffle/run/pools. Dominant species
were sand shiners, black bullheads and green sunfish. Expected dominant fish species for this stream type
would have included flathead chubs, sand shiners, western silvery and plains minnows and fewer
introduced species. Although most fish species expected are present and there were a good number of
river carpsuckers which helped the IBI score. Presence of abundant non-natives (black bullheads and
green sunfish) has shifted the IBI score lower than it would have been, but overall a good fish community.

Fish Community Quality: IBI= 88.05 0/E= 11/11 or 100% of the expected fish community.

Macroinvertebrate Community: This community consists of the Filtering Collector, Prairie Stream
and Large Prairie River assemblage of macro invertebrates (#9, 11, 37 Stagliano 2005). Over 80%) of the
indicator species expected were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 62.5 0/E= >80%

Site Description

Little Missouri River (Site #2, Salmen Ford)

Figure 13. Little Missouri River Site #2 (AES BOO 5)
run/pool habitat near Ladner, SD.

Figure 14. Little Missouri River Site #2 (AES B005)
s auger (Sander canadensis) an SOC in MT but
not SD.

f/'4 \

Figure 15. Little Missouri River Site #2 (AES B005)
goldeyes (Hiodon alosoides) a sensitive
indicator Medium-Large Prairie River fish
species.

Location: Accessed going north on Rt. 867 out of Camp Crook, turn Right at Rt. 988 and proceed 3 mile
to a dirt road on the left beft)re Salmen Ford. Top of reach starts -100m downstream of this ford (see
photo 13) and proceeds -300m downstream to the corner bend.

Nearest Town: Ladner, Harding County, MT

Ecoregion: Northern Great Plains Steppe (Typical)

Aquatic Ecological System Type: B005-Northwestern Great Plains Medium Prairie Stream, borderline
Large Prairie River probably around the ND border.

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
sheep grazing on right bank looking downstream

Rare or Unique Species: The dominance of large river species (goldeyes, sauger and channel catfish)

Rare Features: Cottonwood stand with good recruitment and regeneration.

Introduced/Exotic Species: Northern pike & carp

Overall Ecological Site Condition: Good to Excellent

Reach Summary: The 300 m reach consisted of 3 riffle/run/pool complexes with full flowing water
connectivity and a braided channel around an island. The uppermost pool was -12m wide, -50m long
(averaged 0.5 m deep) and contained the most fish holding habitat, a riffle above this pool was the top of
the reach. This pool was followed by a 50m deep run which divided around an island forming a braided
channel (see photo). This stream reach has excellent aquatic habitat (30% of the channel depths were
>0.5m), and a diversity of microhabitats leading to high fish species diversity (14 species). Pools
averaging 25-40m long and 8- 10m wide. Substrate of the upper pool was gravel-dominated with some silt
and cobbles, and the lower pools dominated by sand/gravel. Aquatic vegetation and overhanging banks at
the margins provided significant stream habitat in this stream reach. Riparian vegetation coverage was
dominated by grasses and shrubs with a significant cottonwood grove with regeneration on the left bank.
Livestock use index (LUI) was moderate with -20 sheep pies counted on a 75m walk of the right bank.

Reach Riparian Ranking: BLM= 90% (22 of 24) EPA RBP= 90% (180 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen C-4 with a
gentle-medium slope (-1%)), moderate sinuosity, and a riffle-pool configuration with substrate dominated
by gravel/cobbles and ranging to gravel-dominated pools. Pools are slightly incised and averaged >40 cm
in depth, wetted width of the reach was 15.4m. Surrounding bank materials are finer than the channel bed
materials.

Amphibian Community: None recorded.

Fish Community: 14 fish species (11 native) were seined in the 3 riffle/run/pools. Dominant species
were goldeyes, sand shiners and channel catfish. Expected dominant fish species for this stream type
would have included flathead chubs, western silvery and plains minnows. Expected fish for this stream
type have been met and included the important species, sauger (Figure 14) and the intolerant goldeye
(Figure 15). The presence of these species substantially raised the IBI scores, and compensated for the
occurrence of 2 introduced species in this river reach, the carp and northern pike. Overall, excellent fish
community.

Fish Community Quality: IBI= 87.6 0/E= 11/11 or 100% of the expected fish community.

Macroinvertebrate Community: This community consists of the Filtering Collector, Prairie Stream
and Large Prairie River assemblage of macro invertebrates (#3, 9, 11, 37 Stagliano 2005). Over 80% of
the indicator species expected were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 72.6 0/E= >80%

Site Description

Little Missouri River (Site #1 Camp Crook)

Figure 16. Little Missouri River Site #1 (AES B005)
run/pool habitat near Camp Crook, SD

Figure 1 7. Little Missouri River Site #1 (AES B005)
run/pool habitat looking upstream

Figure 18. Little Missouri River Site #1 (AES B005)
Cottonwood stand on upper terrace

Location: Accessed going north on Rt. 867 out of Camp Crook, turn Right at dirt road after 1 mile, go 1
mile east until you hit the state section fence and proceed to river. Reach is -100m downstream of this
point and -200m upstream to the top riffle.

Nearest Town: Camp Crook, Harding County, MT

Ecoregion: Northern Great Plains Steppe (Typical)

Aquatic Ecological System Type: B005-Northwestern Great Plains Medium Prairie Stream, borderline
Large Prairie River type-probably changing around the ND border.

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
old grazing on left bank looking downstream

Rare or Unique Species: No rare species or communities documented

Rare Features: Cottonwood stand with good recruitment and regeneration

Introduced/Exotic Species: Green sunfish and common carp

Overall Ecological Site Condition: Good

Reach Summary: The 300 m reach consisted of 1 long riffle/pool/run complex with full flowing water
connectivity (Figure 16). The uppermost pool was 15- 18m wide, -50m long (averaged 0.75m deep) and
contained the most diverse fish species habitat, a riffle above this pool was the top of the reach (Figure
17). This pool was followed by a 150m deep run along the incised left bank. This stream reach has good
aquatic habitat and a fair diversity of microhabitats, leading to high fish species diversity (14 species, 1 1
native). Substrate of the upper pool was gravel and silt-dominated with some cobbles. Geomorphic
structures and overhanging banks provided the most habitat in this stream reach. The riparian channel
within the reach was vegetated on top, but down-cut and provided minimal shading. The incisement of the
outside bend with cottonwoods on the terrace at the top of the reach can be seen in Figure 17. The
upper terrace and floodplain of the left bank has a nice stand of cottonwoods (Figure 18).

Reach Riparian Ranking: BLM= 79% (19 of 24) EPA RBP= 86% (172 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-4 with a
gentle-medium slope (<1%)), moderate sinuosity, a riffle-pool configuration with substrate dominated by
gravel/pebbles and gravel/silt dominated pools. The reach was slightly incised (entrenchment ratio -1 .5)
and averaged -51 cm in depth and average wetted width of the reach was 11.8m. Surrounding bank
materials are finer than the channel bed materials.

Amphibian Community: No amphibians reported from this site.

Fish Community: 14 fish species (11 native) were seined in the riffle/run/pool. Dominant species were
fathead minnows and sand shiners. Expected dominant fish species for this stream type would have
included flathead chubs, sand shiners, western silvery and plains minnows and fewer fatheads. Although,
most fish species expected are present, thus a good O/E score, the presence of non-natives and
dominance of fatheads has caused a lowered IBI score and is ranked as slightly impaired. But overall a
good fish community.

Fish Community Quality: IBI= 65.19 0/E= 10/11 or 92% of the expected fish community.

Macroinvertebrate Community Quality: MT MMI= 63.4 0/E= >80%

Site Description

South Fork Moreau River (site #3)

Figure 19. South Fork Moreau River #3 (AES B005)
pool habitat, looking downstream near Hoover,
SD

Figure 20. South Fork Moreau River #3
(AES B005) run/pool habitat,
looking upstream near Hoover, SD

Figure 21. South Fork Moreau River #3 (AES B005)
exposed layer of dense fossils in right bank

Figure 22. South Fork Moreau River #3 (AES B005)
petrified tree stumps on right bank

Location: Accessed from Route 79, Butte County Road at the bridge crossing and proceeded upstream
-100m to the first pool set designated the bottom of the reach (Figure 19).

Nearest Town: Hoover, Butte County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: B005-Northwestern Great Plains Medium Prairie River

Key Environmental Factors: Hydrology — upstream dams, incised channel; Grazing — slight impacts

Rare or Unique Species: No rare species, but good riparian cottonwood stands in local landscape.

Rare Features: Petrified logs and fossil remains in the right stream bank (Figure 21 Sell).

Introduced/Exotic Species: Green sunfish

Overall Ecological Site Condition: Fair/Good

Reach Summary: The 250m reach consisted of 3 run/pool complexes with the uppermost pool being
-100m long and containing the most fish holding habitat. This stream reach has moderate aquatic habitat
and a diversity of microhabitats, thus leading to high fish species diversity (12 species, 10 native). Pools
averaging 10- 15m long and 2.25m wide. The first 2 riffle/pool complexes proceeding upstream were deep
enough to allow seining for fish, the last pool was clear and shallow enough to visibly inspect for fish and
amphibians. Spacing between the pools was -20m apart for the bottom 3, and -100m from pool 3 to 4.
All substrate of the pools was gravel dominated with some silt and cobbles and pools 1 and 2 with
surrounding vegetation dominated by Scirpus sp. (rushes) and Eleocharis palustris, common spikerush.
Aquatic vegetation and overhanging banks provided the most significant stream habitat in this stream
reach. Livestock use index (LUI) was low with -7 cow pies counted on a 75m walk of the left bank.
Pugging and hummocking was absent in the immediate riparian reach.

Reach Riparian Ranking: BLM= 62.5% (15 of 24) EPA RBP= 64% (128 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-4 with a
gentle-medium slope (-1%)), moderate sinuosity, and a glide-pool configuration with substrate dominated
by silted-cobbles and ranging from silt to gravel-dominated pools. Pools are incised and averaged >40 cm
in depth, wetted width of the reach was 6.8 m. Surrounding bank materials are finer than the channel bed
materials.

Amphibian Community: 1 adult Northern Leopard Frog (NLF) present in the uppermost pool and a
garter snake in the riparian zone.

Fish Community: 11 fish species (9 native) were seined in the 3 run/pools. Dominant species were
fathead minnows and sand shiners. Expected dominant fish species for this stream type would have
included flathead chubs, sand shiners, western silvery and plains minnows and fewer fatheads. Although
most fish species expected are present, thus a good O/E score, the presence of non-natives and
dominance of fatheads has caused a lowered IBI score and is ranked as slightly impaired. But overall a
good fish community.

Fish Community Quality: IBI= 65.19 0/E= 9/11 or 81.8% of the expected fish community.

Macroinvertebrate Community: This community consists of the Filtering Collector, Prairie Stream
and Large Prairie River assemblage of macro invertebrates (#9, 11, 12, 40 Stagliano 2005). This
community was devoid of the filtering collector assemblage indicator species and few indicators of the
Large Prairie River assemblage indicting that the community of this site is incomplete. Only -60% of the
indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 45.6 0/E= 62%

Northwestern Great Plains Prairie Stream Ecological Types

Northwestern Great Plains Prairie Stream (AES COOS) Ecological Types in order of highest biological
integrity to lowest. 1) South Fork Grand #2, 2) South Fork Grand #1,3) North Fork Moreau River #2, 4)
Jones Creek #2, 5) Crooked Creek, 6) South Fork Moreau River #2, 7) Bull Creek

Management/Threats to this ecological system include: Grazing and livestock use around the
riparian areas occurs and can have strong local effects resulting in sedimentation and stream widening at
cattle crossings. Introductions of game or forage fish in stock ponds anywhere in the watershed can
make their way downstream to these perennial prairie rivers and become permanent residents, competing
with (green sunfish) or preying upon (northern pike) resident native fish species.

Global Rank Comments: The number of viable occurrences is unknown, but probably rare. Although,
these systems occur higher in the watershed, and not as rare as a high quality Medium Prairie River.
These prairie river ecological types are abundant in terms of river miles across the Northern Great Plains
Steppe of North America, but the hydrology (i.e. water permanence) can be easily affected by upstream
dams or diversions in the watershed. Stock ponds that are stocked with game fish, and bait bucket
introductions can also contribute to the community degradation brought about by the introduced fish
species.

Site Description

South Fork Grand River (site #2) (on report cover)

Figure 23. South Fork Grand River #2 (AES 0005)
with reference condition landscape and local-
reach overview from bridge

Figure 24. South Fork Grand River #2 (AES C005) Figure 25. South Fork Grand River #2 (AES C005)

bottom of reach looking upstream bottom of reach looking downstream

Location: Accessed from Rt. 79 at bridge crossing and proceeded upstream -100m to the first riffle/
pool set designated the bottom of the reach.

Nearest Town: Reva, Harding County, SD

Ecoregion: Northern Great Plains Steppe (Typical)

Aquatic Ecological System Type: C005-Northwestern Great Plains Prairie Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
slight impacts

Rare or Unique Species: No rare species, but excellent fish community

Rare Features: Excellent Prairie Stream Habitat

Introduced/Exotic Species: Black bullhead and green sunfish (rare)

Overall Ecological Site Condition: Good to Excellent

Reach Summary: The 300 m reach consisted of 3 riffle/run/pool complexes with full flowing water
connectivity. The uppermost pool was -30m long and contained the most fish holding habitat. This stream
reach has excellent aquatic habitat and a diversity of microhabitats, thus leading to high fish species
diversity (11 species, 9 native). Pools averaging 20-25m long and 4.5m wide. The first 2 riffle/pool
complexes proceeding upstream were the deeper habitat for fish seining, the last pool shallow enough to
visibly inspect for fish and amphibians. Spacing between the pools was -20m apart for the bottom 3, and
-100m from pool 3 to 4. All substrate of the pools was gravel dominated with some silt and cobbles.
Aquatic geomorphic features and overhanging banks provided the most significant stream habitat in this
reach. Vegetation coverage along the riparian stream channel was dominated by grasses and fully intact.
Livestock use index (LUI) was low with 10 cow pies counted on a 75m walk of both left and right banks.

Reach Riparian Ranking: BLM= 95.8% (23 of 24) EPA RBP= 94.5 % (189 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen C-3b with a
gentle-medium slope (-1%), moderate sinuosity, a riffle-pool configuration with substrate dominated by
cobbles and ranging to gravel-dominated pools. Pools are slightly incised and averaged >40 cm in depth,
wetted width of the reach was 8.2. Surrounding bank materials are finer than the channel bed materials.

Amphibian Community: 1 adult Woodhouse's toad present along the uppermost pool.

Fish Community: 12 fish species were seined in the 3 riffle/run/pools. Dominant species were the
flathead chubs, plains minnows and sand shiners. Expected fish for this stream type would have been
fathead minnows and brook sticklebacks, so the brassy minnows were a nice surprise.

Fish Community Quality: IBI= 103.6 0/E= 9/7.75 or 116% of the expected fish community.

Macroinvertebrate Community: This community consists of the Filtering Collector, Prairie Stream
and Large Prairie River assemblage of macro invertebrates (#9, 11, 37 Stagliano 2005). Over 80% of the
indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 79.7 0/E= >80%

Site Description

South Fork Grand River (site #1)

Figure 26. South Fork Grand River #1 (AES COO 5)
looking downstream towards county bridge

Figure 27. South Fork Grand River #1
(AES C005) bottom riffle of reach
looking upstream

Figure 28. South Fork Grand River #1 (AES C005)
top 150m long pool

Figure 29. South Fork Grand River #1 (AES C005)
catfish seined in the top pool

Location: Accessed from County Road (Old Route 20) 12.5 miles northeast from at the bridge crossing
(Figure 26) and proceeded upstream above vehicle ford to the first riffle/pool set designated the bottom of
the reach (Figure 27).

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: C005-Northwestern Great Plains Perennial Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in tributaries of the watershed;
Grazing — slight impacts

Rare or Unique Species: No rare species, but an excellent fish community

Rare Features: No rare features documented

Introduced/Exotic Species: Black bullhead and green sunfish (rare)

Overall Ecological Site Condition: Good to Excellent

Reach Summary: The 300 m reach consisted of 3 riffle/run/pool complexes (full flowing connectivity)
with the uppermost pool being -100m long and containing the most fish holding habitat. This stream reach
has excellent aquatic habitat and a diversity of microhabitats, thus leading to high fish species diversity (12
species, 10 native). Pools averaging 10- 15m long and 2.25m wide. The first 2 riffle/pool complexes
proceeding upstream were deep enough to allow seining for fish, the last pool was clear and shallow
enough to visibly inspect for fish and amphibians. All substrate of the pools was gravel dominated with
some silt and cobbles and pools 1 and 2 with surrounding vegetation dominated by Scirpus sp. (rushes)
and Eleocharis palustris, common spikerush. Aquatic vegetation and overhanging banks provided the
most significant stream habitat in this stream reach. Grasses, although sparse in places (Figure 26),
comprised a large percentage of vegetation coverage along the riparian stream channel. Livestock use
index (LUI) was moderate with -20 cow pies counted on a 75m walk of the left bank. Pugging and
hummocking was minimal.

Reach Riparian Ranking: BLM= 95.8% (23 of 24) EPA RBP= 93.5 % (188 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen C-3b with a
gentle-medium slope (-1.5%), moderate sinuosity, a riffle-pool configuration with substrate dominated by
cobbles and ranging to gravel-dominated pools. Pools are slightly incised and averaged >40 cm in depth,
wetted width of the reach was . Surrounding bank materials are finer than the channel bed materials.

Amphibian Community: 1 Adult Northern Leopard Frog (NLF) observed in the uppermost pool.

Fish Community: 12 fish species (9 native) were seined in the 3 riffle/run/pools. Dominant species
were the flathead chubs, plains minnows and sand shiners. Expected fish for this stream type have been
met, although a couple of introduced species were present (black bullhead and green sunfish). These
probably originated from the Jones Creek stock pond reservoirs that can contribute introduced species
during high flow events.

Fish Community Quality: IBI= 99.8 0/E= 9/7.75 or 116%) of the expected fish community.

Macroinvertebrate Community: This community consists of the Filtering Collector, Prairie Stream
and Large Prairie River assemblage of macro invertebrates (#9, 11, 37 Stagliano 2005). The expected
community indicator species are present and this site ranked high with the MT MML Over 80% of the
indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 69.8 0/E= >80%

Site Description

North Fork Moreau River (site #2)

Figure 30. North Fork Moreau River
(AES C005) Marty Bridge site not
sampled

Figure 31. North Fork Moreau River #2 (AES COOS)
upper riffle looking downstream

Figure 32. North Fork Moreau River #2
(AES C005) bottom of reach
looking upstream

Location: Accessed from Rt 79 bridge, 1.2 miles north of County Rd. 732 and proceeded upstream
-200 m to the bottom set of pools. Another site in the vicinity was visited off the Marty Rd. bridge (Figure
30), which appeared to be similar in geomorphology and condition to this site, but was not sampled.

Nearest Town: Hoover, Butte County, SD

Ecoregion: Northwestern Great Plains (Typical)

Aquatic Ecological System Type: C005-Northwestern Great Plains Perennial Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
slight impacts

Rare or Unique Species: No rare species or communities documented

Rare Features: No rare features documented

Introduced/Exotic Species: Black bullhead, golden shiner and green sunfish (all rare)

Overall Ecological Site Condition: Good

Reach Summary: The 300 m reach consisted of 2 riffle/run/pool complexes (full flowing connectivity)
with the lowermost pool being -1 00m long, -40cm deep and containing the most fish holding habitat. This
stream reach has moderate quality habitat and a fair diversity of microhabitats, thus leading to high fish
species diversity (11 species, 8 native). All substrate of the top riffle/run was gravel dominated with some
silt and cobbles and pools 1 and 2 with surrounding vegetation dominated by Scirpus sp. (rushes) and
Eleocharis palustris, common spikerush (Figure 31). Aquatic geomorphic features and overhanging
banks provided the most significant stream habitat in this stream reach. Vegetation coverage along the
riparian stream channel was largely intact and dominated by grasses. Livestock use index (LUI) was low
with -10 cow pies counted on a 75m walk of the left & right banks. Pugging and hummocking was
minimal.

Reach Riparian Ranking: BLM= 95% (23 of 24) EPA RBP= 89% (178 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen C-4 with a
gentle-medium slope (-1%)), moderate sinuosity, a riffle/run/pool configuration with substrate dominated
by gravels & cobbles and ranging to gravel to silt-dominated pools. Pools are slightly incised and averaged
>40 cm in depth, wetted width of the reach was 4.4m. Surrounding bank materials are finer than the
channel bed materials and the bluff bank upstream (Figure 32) probably contributes sediments in high
flow events.

Amphibian Community: 1 adult Northern Leopard Frog (NLF) observed in the uppermost pool.

Fish Community: 11 fish species (8 native) were seined in the 2 riffle/run/pools. Dominant species
were the plains minnows, sand shiners and flathead chubs, which are the expected fish for this stream
type. Although a few introduced species were present (black bullhead, golden shiners and green sunfish),
they were not abundant and did not have a large detrimental effect on the IBI, which was an excellent
score.

Fish Community Quality: IBI= 90.3 0/E= 8/7.5 or 103%) of the expected fish community.

Macroinvertebrate Community: This community consists of the Filtering Collector, Prairie Stream
and Large Prairie River assemblage of macro invertebrates (#9, 11, 37 Stagliano 2005). Over 80% of the
indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 57.1 0/E= >80%

Site Description

Jones Creek (site #2)

Figure 33. Jones Creek #2 (AES C005)
pool upstream from road crossing

Figure 34. Jones Creek #2 (AES COOS)
pools below the road crossing

Figure 35. Jones Creek #2 (AES C005) typical
green sunfish, an introduced species

Figure 36. Jones Creek #2 (AES C005) riffle
downstream from road crossing

Location: Accessed from County Road (Old Route 20) 12.5 miles northeast from Buffalo, SD,
approximately Vi mile before the old S.F. Grand Bridge crossing. Then heading north a tenth of a mile on
a 2-track to a stream crossing and proceeded upstream -10m to the first pool and downstream 100m for
the bottom series of pools of the reach.

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: COOS-Northwestern Great Plains Perennial Stream, but due to
reduced hydrology from upstream dams, trending towards a D005 Northwestern Great Plains Intermittent
Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
moderate impacts

Rare or Unique Species: No rare species or communities documented

Rare Features: No rare features documented

Introduced/Exotic Species: Black & yellow bullhead, green sunfish

Overall Ecological Site Condition: Good- with high restoration potential

Reach Summary: The 150 m reach consisted of a 50m run/pool complex above the road crossing and a
100m series of riffle/run/pools below the crossing. This road crossing could really use a culvert, as the dirt
fill road is causing hydro logic modifications and accumulating silt in the upper pool. The upper pool being
-30m long and 5m wide contained the deepest fish habitat, albeit silted (Figure 33). This stream reach has
moderate-quality aquatic habitat and good fish species diversity (8 fish species, 5 natives). Pools below
the road averaged 5- 10m long and 2.25m wide (Figure 34). Spacing between the pools was fully
connected. All substrate of the pools was silt dominated with some gravel/pebble in the runs between
them; the lower pools contain pebble/cobble riffle areas between them (Figure 36), which provided the
highest habitat diversity for macroinvertebrates. The surrounding vegetation dominated by Scirpus sp.
(rushes) and Eleocharis palustris, common spikerush. Aquatic vegetation and overhanging banks
provided the most significant stream habitat in this stream reach. Livestock use index (LUI) was
moderate with -15 cow pies counted on a 75 m walk of the left bank. Pugging and hummocking was
minimal.

Reach Riparian Ranking: BLM= 80% (20 of 24) EPA RBP= 87.5% (175 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen E-4 with a
gentle-medium slope (-1%)), moderate sinuosity, a riffle-pool configuration with substrate dominated by
gravels and silted-embedded pools. Pools are slightly incised and averaged >30 cm in depth, wetted width
of the reach was 3.4. Surrounding bank materials are similar to the channel bed materials indicating a
balance of sediment accumulation locally and upstream in the reach, except for the hydrologic change
caused by the road crossing.

Amphibian Community: 1 Adult Northern Leopard Frog (NLF) present in the uppermost pool.

Fish Community: 8 fish species (5 natives) were seined in the 2 riffle/run/pool sequences. Dominant
species were the sand shiners, fathead minnows and flathead chubs. Expected fish for this stream type
have almost been met, although a few introduced species were present (Black/Yellow Bullhead and green
sunfish (Figure 35)). These probably originated from the upstream Jones Creek stock ponds that can
contribute introduced species during high flow events. Only the one introduced species (green sunfish)
was seined below the road, possibly indicating the road may be a barrier to bullhead from getting
downstream.

Fish Community Quality: IBI= 88.25 0/E= 5/7.5 or 66.7% of the expected fish community.

Macroinvertebrate Community: This community of intermittent prairie stream invertebrates consisted
of the Prairie Pool assemblage (#12, Stagliano 2005) and the Prairie Stream assemblage found in the
cobble riffle areas (#9, Stagliano 2005). Over 80% of the indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 58.9 0/E= >80% of the expected
community.

Site Description

Crooked Creek (tributary to the North Fork Grand)

Figure 37. Crooked Creek (AES COO 5)
looking upstream near Cox Church

Location: Accessed from County Rd. 733 @ Cox Church, 7 miles west of Rt 85, -20 miles north of
Buffalo.

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: C005-Northwestern Great Plains Perennial Stream, but due to
reduced hydrology from upstream dams, trending towards a D005 Northwestern Great Plains Intermittent
Stream

Key Environmental Factors: Hydrology — upstream and downstream dams in the watershed; Oil and
gas drilling in the watershed; Grazing — slight impacts

Rare or Unique Species: No rare species documented

Rare Features: No rare features documented

Introduced/Exotic Species: Black bullhead & green sunfish (rare, not abundant)

Overall Ecological Site Condition: Fair/Good

Reach Summary: The 100 m reach consisted of 1 run/pool complex with the pool being -90m long and
fairly incised (Figure 37). This site contains no riffle or erosional areas decreasing the ability to provide
habitat for other COOS fish species. The stream reach has decent aquatic habitat and is set in a quality

local landscape. But the water quality or some other factor is definitely affecting the fish community's
low integrity ratings. All substrate of the reach was silt dominated with some cobble associated with the
bridge. Adjacent riparian vegetation was dominated by Eleocharis palustris, the common spikerush and
grasses which provided excellent bank stability (Figure 37). Aquatic submerged vegetation provided the
most significant stream habitat in this reach contributing to the abundant brook sticklebacks. Livestock
use index (LUI) was low here with zero cow pies counted on a 50 m walk of the left & right banks.
Pugging and hummocking was absent.

Reach Riparian Ranking: BLM= 66.7% (16 of 24) EPA RBP= 67.5% (135 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F6 with a
gentle slope (<!%>), low sinuosity, a run-pool configuration with silt-dominated runs and pools. Pools are
slightly incised and averaged -30 cm in depth, wetted width of the reach averaged 5m. Surrounding bank
materials are similar to the channel bed materials indicating a balance of accumulation locally and
upstream in the reach.

Amphibian Community: 20 Adult Northern Leopard Frog (NLF) present. Undetermined toad, Bufo
sp., tadpoles (prob. Woodhouse's) also present in pool.

Fish Community: 5 fish species (3 natives) were seined in the pools. Dominant species are the fathead
minnow and brook stickleback and the white sucker was also present. Expected fish for this stream type
have not been met, and the fish IBI is showing moderate impairment. This indicates that habitat quality or
water quality are definitely affecting the fish community.

Fish Community Quality: IBI= 49.5 0/E= 2/2.4 or 83% of the expected indicator fish species.

Macroinvertebrate Community: This community of prairie stream invertebrates consists of the
Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are characterized by
tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and Ishnura, the
crustaceans {Hyalella and Gammarus), many genera and species of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles {Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Over 80% of the indicator species were present in this
sample.

Macroinvertebrate Community Quality: MT MMI= 39.5 0/E= 80%

Site Description

South Fork Moreau River (site #2)

Figure 38. South Fork Moreau River #2
(AES COOS) pool habitat, looking
upstream near Rte. 85 bridge

!IM

■Illujl

f *1

^^^^^

^^^^

Figure 39. South Fork Moreau River #2 (AES COOS)
pool habitat, top of reach

Figure 40. South Fork Moreau River #2
(AES COOS) pool habitat,
Cottonwood trees top of reach

Location: Accessed from Rt 85, -10 miles south of Redig at the bridge crossing and proceeded
upstream (west) -50m to the first pool set designated the bottom of the reach (Figure 38).

Nearest Town: Redig, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: C005-Northwestern Great Plains Perennial Stream

Key Environmental Factors: Hydrology — upstream beaver dams; Grazing — slight impacts;
Geomorphology — incised channel, unconsolidated substrate

Rare or Unique Species: Iowa darters were documented at the downstream end of reach.

Rare Features: Dead sheep hanging in a tree near top of reach, shows hydrologic extremes (Figure 40)

Introduced/Exotic Species: Dominated by Black bullhead and green sunfish

Overall Ecological Site Condition: Poor/Fair

Reach Summary: The 300 m reach consisted of 1 long pool complex with the uppermost 100m of the
pool being deepest and most incised (Figure 39). There were some areas of submerged aquatic
vegetation that provided most of the fish holding habitat, but unconsolidated knee-deep silt and chest-deep
(1-1. 5m) channel depths made seining difficult. This stream reach has been overtaken by introduced
species and the aquatic habitat is not conducive to a typical COOS fish community (e.g.. no stable
substrate). All substrate of the pools was silt dominated with some clay. Riparian vegetation was
dominated by shrubs & grasses, but there were a few dying cottonwoods on the right bank (Figure 39,
40). Aquatic vegetation and overhanging banks provided the most significant stream habitat in this stream
reach. Livestock use index (LUI) was moderate with -20 cow pies counted on a 75m walk of the left
bank. Pugging and hummocking was especially noticeable in the lower pool area where the cows have a
stream crossing.

Reach Riparian Ranking: BLM= 50% (12 of 24) EPA RBP= 47.5 % (97 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen G-6 with a
gentle slope (-0.5%), moderate sinuosity, an unstable, degrading run-pool configuration with
unconsolidated, erodible substrate dominated silts and clays. Pools are moderately incised and averaged
>75 cm in depth, wetted width of the reach was 4.5m. Surrounding fine bank materials are similar to the
channel bed materials and riparian vegetation needs to be dense to provide bank stabilization (Figure 39).

Amphibian Community: 1 adult Northern Leopard Frog (NLF) present in the uppermost pool.

Fish Community: 5 fish species (3 native) were seined in the 300m pool complex. Dominant species
were fathead minnows and black bullheads. Expected fish for this stream type would be flathead chubs,
plains minnows and sand shiners so the expected community was not met.

Fish Community Quality: IBI= 34.9 0/E= 38.7% of expected fish community.

Macroinvertebrate Community: This community was dominated by the intermittent prairie stream
invertebrates of the Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species
should have contained members of the Prairie Stream macro invertebrates (#9 Stagliano 2005). Only 40%
of the indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI=22.3 O/E=40%) of expected macro community.

Site Description

Bull Creek (tributary to the South Fork Grand)

Figure 41. Bull Creek (AES COO 5) a silt-impaired
Great Plains stream near Brown Rd.

Location: Accessed from County Rd. 733, 7 miles west of Rt 85, -20 miles northwest of Buffalo.

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: C005-Northwestern Great Plains Perennial Stream, but due to
reduced hydrology from upstream dams, trending towards a D005 Northwestern Great Plains Intermittent
Stream

Key Environmental Factors: Hydrology — upstream and downstream dams in the watershed; cattle
grazing in the watershed

Rare or Unique Species: No rare species documented

Rare Features: No rare features documented

Introduced/Exotic Species: None

Overall Ecological Site Condition: Poor/Fair

Reach Summary: The 100 m reach consisted of 1 run/pool complex with the pool being -90m long and
fairly incised (Figure 41). This site contains no riffle or erosional areas decreasing the ability to provide
habitat for other COOS fish species. The stream reach has intact riparian habitat and is set in a quality
local landscape. But the channel condition and accumulation of silt is definitely affecting the fish and
macroinvertebrate community's low integrity ratings. Bottom substrate of the reach was 0.5m deep,
unconsolidated silt, which made sampling difficult. The immediate surrounding vegetation was dominated
by Scirpus sp. (rushes) and Eleocharis palustris, common spikerush. Riparian zone consisted entirely of
grasses. Livestock use index (LUI) was low with 5 cow pies counted on a 50 m walk of the left & right
banks. Pugging and hummocking was minimal.

Reach Riparian Ranking: BLM= 50% (12 of 24) EPA RBP= 55% (110 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-6 with a
gentle slope (<1%)), low sinuosity, a run-pool configuration with silt-dominated runs and pools. Pools are
slightly incised and averaged -40 cm in depth, wetted width of the reach averaged 5m. Surrounding bank
materials are coarser than the channel bed materials indicating an accumulation of sediments locally and
upstream in the reach.

Amphibian Community: 2 adult Northern Leopard Frog (NLF) were recorded.

Fish Community: 2 fish species (1 native) were seined in the pool. Dominant species was the fathead
minnow. Expected fish for this stream type have not been met, and the fish TBI is showing moderate
impairment. This indicates that habitat quality or water quality are definitely affecting the fish community.

Fish Community Quality: IBI= 43.6 0/E= 50%) of the expected indicator fish species.

Macroinvertebrate Community: This community of prairie stream invertebrates consists of the
impaired Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are
characterized by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and
Ishnura, the crustaceans (Hyalella and Gammarus), many genera of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Only 50% of the indicator species were present in this
sample.

Macroinvertebrate Community Quality: MT MMI= 24.8 0/E= 50%

Intermittent Prairie Stream Ecological Types

Intermittent Prairie Stream Ecological Types (AES code D005) in order of highest biological integrity to
lowest. 1) North Fork Moreau site #1,2) South Fork Moreau site #1 ; 3) Campbell Creek, 4) Spur Creek, 5)
Hay Creek, 6) Jones Creek #1

Management/Threats: Grazing and livestock use around the riparian areas occurs and can have strong
local effects resulting in sedimentation and stream widening at cattle crossings. This can be especially
detrimental during the non-connective, drying period when intensive riparian cattle usage can trample
banks, and hummock saturated soils having implications for downstream connectivity the following year.
Hydrology can be easily affected in this ecological system by upstream dams or diversions in the
watershed because it is on such a tenuous edge of existence.

Global Rank Comments: The number of viable occurrences is unknown, but probably abundant.
These prairie stream ecosystems are abundant across the Northern Great Plains Steppe of North
America, but the hydrology (i.e. water permanence) can be easily affected by upstream dams or
diversions in the watershed. Stock ponds that are stocked with game fish can also contribute to the
community degradation of introduced fish species.

Site Description

North Fork Moreau River (site #1)

Figure 42. North Fork Moreau River #7
(AES D005) pool #3 looking
upstream

Figure 43. North Fork Moreau River #1
(AES D005) pool #2 looking
upstream

Location: Accessed from Rt 85 bridge and proceeded upstream to the first set of pools.

Nearest Town: Redig, Harding County, SD

Ecoregion: Northwestern Great Plains

Aquatic Ecological System Type: D005-Northwestern Great Plains Intermittent Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
moderate impacts

Rare or Unique Species: No rare species or communities documented

Rare Features: No rare features documented

Introduced/Exotic Species: Smooth brome was documented

Overall Ecological Site Condition: Fair

Reach Summary: The 300 m reach contained 4 pools averaging 10- 15m long and 2.25m wide and
lacked connectivity. The first 3 proceeding upstream were deep enough to allow seining for fish, the last
pool was clear and shallow enough to visibly inspect for fish and amphibians. Spacing between the pools
was -20m apart for the bottom 3, and -100m from pool 3 to 4. All substrate of the pools was silt and fine
sediments (<2mm) and pools 1 and 2 contained Typha latifolia stands with surrounding vegetation

dominated by Scirpus sp. (rushes) and Eleocharis palustris, common spikemsh. Aquatic vegetation and
overhanging banks provided the most significant stream habitat in this stream reach. Equisetum sp.
(Horsetails) also comprised a large percentage of vegetation coverage along the riparian stream channel
between pools 2-4. Livestock use index (LUI) was moderate with -20 cow pies counted on a 75m walk
of the left bank. Pugging and hummocking was especially noticeable in the first pool area where the cows
have a stream crossing, and upstream at the 275m mark just below pool 4.

Reach Habitat Ranking: BLM= 71 % (17 of 24) EPA RBP= 80 % (160 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is roughly a Rosgen E-6
with a gentle slope (<2%), moderate sinuosity, a glide-pool configuration and substrate ranging from silt-
dominated pools and sand to pebbles in the dried connecting glides. Pools are quite incised and averaged
>50 cm in depth.

Amphibian Community: 1 adult Northern Leopard Frog, Rana pipiens (NLF) present. Evidence of
breeding amphibians was present in NLF and Great Plains Toad, Bufo cognatus tadpoles.

Fish Community: 2 fish species (Fathead and brassy minnows) were seined in the 3 pools. Expected
dominant fish for this stream type would have been fathead minnows and brook sticklebacks, so the
brassy minnows were a nice surprise.

Fish Community Quality: IBI= 51.5 0/E= 2/2.4 or 75% complete.

Macroinvertebrate Community: This community of prairie stream invertebrates consists of the
impaired Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are
characterized by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and
Ishnura, the crustaceans {Hyalella and Gammarus), many genera of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Only 60% of the indicator species were present in this
sample.

Macroinvertebrate Community Quality: MT MMI= 28 0/E= 60%

Site Description

South Fork Moreau River (site #1)

^^PP^*'"

Figure 44. South Fork Moreau River #1
(AES D005) vegetative pool habitat,
looking from bridge

-^&

^^-^'^^

W^^^lll^

''f ■

■ -4^ -

^Ji^\

Figure 45. South Fork Moreau River #1
(AES D005) beaver dam pool
habitat

Figure 46. South Fork Moreau River #1
(AES D005) pool habitat looking
up

Location: Accessed from Butte County Road at the bridge crossing -3 miles west of Rte. 85 and
proceeded upstream to the first pool set designated the bottom of the reach.

Nearest Town: Redig, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: D005-Northwestern Great Plains Intermittent Stream trending
towards a Great Plains prairie stream if downstream connectivity is maintained.

Key Environmental Factors: Hydrology — upstream beaver dams; Grazing — moderate impacts

Rare or Unique Species: Iowa Darter

Rare Features: No rare features documented

Introduced/Exotic Species: Yellow bullhead, golden shiner and green sunfish

Overall Ecological Site Condition: Fair

Reach Summary: The 250m reach consisted of 3 run/pool complexes with the uppermost pool being
-100m long and containing the most fish holding habitat. This stream reach has moderate aquatic habitat
with extensive beds of macrophytes, beaver dam complexes in the reach, without which, the pool would
have been smaller and disconnected. Pools averaging 10- 15m long and 2.25m wide. The first 2 riffle/pool
complexes proceeding upstream were deep enough to allow seining for fish, the last pool was clear and
shallow enough to visibly inspect for fish and amphibians. Spacing between the pools was -20m apart for
the bottom 3, and -100m from pool 3 to 4. All substrate of the pools was silt dominated with surrounding
vegetation dominated by Scirpus sp. (rushes) and Eleocharis palustris, common spikerush. Aquatic
vegetation and overhanging banks provided the most significant stream habitat in this stream reach.
Livestock use index (LUI) was moderate with -20 cow pies counted on a 75m walk of the left bank.
Pugging and hummocking was especially noticeable in the first pool area where the cows have a stream
crossing near the beaver dam.

Reach Riparian Ranking: BLM= 66.7% (16 of 24) EPA RBP= 69.5 % (139 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-6 with a
gentle-medium slope (-1%), moderate sinuosity, a run-pool configuration with substrate dominated by
cobbles and ranging to gravel-dominated pools. Pools are slightly incised and averaged >40 cm in depth,
wetted width of the reach was . Surrounding bank materials are finer than the channel bed materials.

Amphibian Community: 20-30 adult Northern Leopard Frogs (NLF) were collected throughout the
reach.

Fish Community: 7 fish species (4 natives) were seined in the 3 pools. Dominant fish species was the
fathead minnow. Expected fish for this stream type would have been fathead minnows, brassy minnows
and brook sticklebacks, so the additional species were a surprise, especially the Iowa darter, unfortunately
3 non-native species were collected reducing the quality of the fish community and the IBL

Fish Community Quality: IBI= 56.65 0/E= 51.6%

Macroinvertebrate Community: Macroinvertebrate Community: This community of intermittent
prairie stream invertebrates consists of the Prairie Pool assemblage (#12, Stagliano 2005). The
community indicator species are characterized by tolerant, damselfly taxa, Coenagrion/Enallagma sp.
Enallagma civile, Lestes and Ishnura, the crustaceans {Hyalella and Gammarus), many genera and

species of the water boatman (Corixidae: Sigara alternate, Trichocorixa nais, and Coriselld), the
snails {Physella, Gyraulus, and Stagnicola), mayflies (Caenis and Callibaetis), and beetles
{Oreodytes, Laccophilus, Hydroporus and Hygrotus). As the complexity of the pool habitat decreases
the dinger habitat species are lost, such as the damselflies and many of the water boatman taxa. Only
65% of the indicator species were present in this sample.

Macroinvertebrate Community Quality: MT MMI= 35.6 0/E= 65%

Site Description

Campbell Creek (tributary to Bull Creek, South Fork Grand)

Figure 47. Campbell Creek (AES D005) pool looking Figure 48. Campbell Creek (AES D005) pool looking
downstream towards Brown 's Pond upstream towards inlet

Location: Accessed from Johnson Rd. 4.5 miles NW of Rt 85. Follow until you reach the National
Forest section and drop in upstream of Brown's Pond.

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Northern Great Plains Steppe

Aquatic Ecological System Type: D005-Northwestern Great Plains Intermittent Stream

Key Environmental Factors: Hydrology — upstream and downstream dams in the watershed;
Grazing — slight impacts

Rare or Unique Species: No rare species documented

Rare Features: No rare features documented

Introduced/Exotic Species: None

Overall Ecological Site Condition: Good

Reach Summary: The 50 m reach consisted of 1 run/pool complex with the pool being -45m long and
backed up as the top of Brown's Pond goes from lotic to lentic. This site is fully on National Forest
ownership. The stream reach has decent aquatic habitat and low species diversity (2 fish species), but
the brook sticklebacks were abundant. All substrate of the reach was silt dominated with some embedded
gravel in the run upstream. The surrounding vegetation was dominated by Scirpus sp. (rushes) and
Eleocharis palustris, common spikerush. Aquatic vegetation provided the most significant stream
habitat in this reach. Livestock use index (LUI) was low here with 10 cow pies counted on a 50 m walk
of the left & right banks. Pugging and hummocking was especially noticeable upstream of the fence
separating the lower pool area from the actual stream inflow.

Reach Habitat Ranking: BLM= 71% (17 of 24) EPA RBP= 74% (148 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F6 with a
gentle slope (<1%)), low sinuosity, a run-pool configuration with silt-dominated runs and pools. Pools are
slightly incised and averaged -30 cm in depth, wetted width of the reach averaged 5m. Surrounding bank
materials are similar to the channel bed materials indicating a balance of accumulation locally and
upstream in the reach.

Amphibian Community: 20 adult Northern Leopard Frog (NLF) present. Undetermined toad, Bufo
sp., tadpoles (prob. Woodhouse's) also present in pool.

Fish Community: 2 fish species were seined in the pool. Dominant species was the brook stickleback
and the fathead minnow was also present. Expected fish for this stream type have almost been met,
although the fish TBI is still showing slight impairment.

Fish Community Quality: IBI= 62.05 0/E= 2/2.4 or 83%) of the expected indicator fish species.

Macroinvertebrate Community: This community of intermittent prairie stream invertebrates consists
of the Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are characterized
by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and Ishnura, the
crustaceans (Hyalella and Gammarus), many genera and species of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Over 80%) of the indicator species were present in this
sample.

Macroinvertebrate Community Quality: MT MMI= 35.6 0/E= 80%

Site Description

Spur Creek (tributary to the South Fork Moreau)

Figure 49. Spur Creek (AES D005) a
tributary to South Fork Moreau
River looking upstream

Figure 50. Spur Creek (AES D005) a

backed up section behind a culvert

Location: Accessed from County Rd. 3 miles west of Rt. 85 at bridge crossing and proceeded upstream
-50m to the first pool area away from the culvert effects in the reach.

Nearest Town: Redig, Butte County, SD

Ecoregion: Typical Northern Great Plains Steppe

Aquatic Ecological System Type: D005-Northwestern Great Plains Intermittent Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
moderate impacts

Rare or Unique Species: Marbled Godwit nesting pair

Rare Features: No rare features documented

Introduced/Exotic Species: None

Overall Ecological Site Condition: Fair

Reach Summary: The 100 m reach consisted of 1 run/pool complex with the lower pool being -70m
long and produced by an earthen uprising near the road culvert and containing the deepest fish holding
habitat This stream reach has sparse aquatic habitat and low species diversity (1 fish species). The first
run proceeding upstream was shallow (-25cm), but deep enough to allow seining for fish (Figure 49) and

abundant fathead minnows were captured. All substrate of the pools was silt dominated with some
embedded gravel in the run upstream. The surrounding vegetation was dominated by Scirpus sp. (rushes)
and Eleocharis palustris, common spikerush. Aquatic vegetation and overhanging banks provided the
most significant stream habitat in this stream reach. Livestock use index (LUI) was moderate with -12
cow pies counted on a 50 m walk of the left & right banks. Pugging and hummocking was especially
noticeable below the lower pool area where the cows have a stream crossing.

Reach Riparian Ranking: BLM= 75% (18 of 24) EPA RBP= 75% (150 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-6 with a
gentle slope (<!%>), moderate sinuosity, a riffle-pool configuration with silt-dominated runs and pools.
Pools are slightly incised and averaged -25 cm in depth, wetted width of the reach averaged Im.
Surrounding bank materials are coarser than the channel bed materials indicating an accumulation of
sediments in the reach.

Amphibian Community: 5 adult Northern Leopard Frog (NLF) present.

Fish Community: 1 fish species was seined in the pool, none in the run. Only species was the fathead
minnow. Expected fish for this stream type (D005 trending toward E005) have been met.

Fish Community Quality: IBI= 48.08 0/E= 1/1.4 or 71%) of the expected reference fish.

Macroinvertebrate Community: This community of intermittent prairie stream invertebrates consists
of the Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are characterized
by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and Ishnura, the
crustaceans {Hyalella and Gammarus), many genera and species of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Only 60% of the indicator species were present in this
sample for a D005 stream type indicating slight impairment. The Montana MMI ranks the community as
slightly impaired as well.

Macroinvertebrate Community Quality: MT MMI= 34.9 0/E= 60% of expected
macroinvertebrates

Site Description

Hay Creek (tributary to the South Fork Moreau)

Figure 51. Hay Creek (AES D005) a tributary to South Figure 52. Hay Creek (AES DO 05) aquatic water -
Fork Moreau River looking upstream plantain (Alisma trivial e)

Location: Accessed from County Rd. 2 miles west of Rt. 85 at bridge crossing and proceeded upstream
-25m to the first pool designated the bottom of the reach.

Nearest Town: Redig, Butte County, SD

Ecoregion: Typical Northern Great Plains Steppe

Aquatic Ecological System Type: D005-Northwestern Great Plains Intermittent Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
moderate impacts

Rare or Unique Species: Aquatic water-plantain, Alisma triviale (Figure 52).

Rare Features: No rare features documented

Introduced/Exotic Species: None

Overall Ecological Site Condition: Fair

Reach Summary: The 100 m reach consisted of 1 run/pool complex with the lower pool being -80m
long and produced by an earthen uprising near the road culvert. This contained the deepest fish holding
habitat. This stream reach has sparse aquatic habitat and low species diversity (1 fish species, low
numbers). Only 8 fathead minnows were captured after multiple seine hauls. All substrate of the pools
was silt dominated with abundant growth of the water-plantain, Alisma gramineum (Figure 52). This was
the only site of all site visits that contained this wetland obligate plant. The riparian vegetation was
dominated by Scirpus sp. (rushes) and Eleocharis palustris, common spikerush. Aquatic vegetation and
overhanging banks provided the most significant stream habitat in this stream reach. Livestock use index
(LUI) was moderate with -15 cow pies counted on a 50 m walk of the left & right banks. Pugging and

hummocking was especially noticeable below the lower pool area where the cows have a stream
crossing.

Reach Riparian Ranking: BLM= 66.7% (16 of 24) EPA RBP= 63% (126 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-6 with a
gentle slope (<1%)), moderate sinuosity, a run-pool configuration with silt-dominated pools. Pools are
slightly incised and averaged -25 cm in depth, wetted width of the reach averaged 4.5 m. Surrounding
bank materials are coarser than the channel bed materials indicating an accumulation of sediments in the
reach.

Amphibian Community: 15-20 adult Northern Leopard Frogs (NLF) were present. No tadpoles were
present in pool.

Fish Community: 1 fish species was seined in the pool, none in the run. Only species was the fathead
minnow. Expected fish for this stream type (D005 trending toward E005) have been met.

Fish Community Quality: IBI= 44.77 0/E= 1/1.4 or 71%) of the expected reference fish.

Macroinvertebrate Community: This community of intermittent prairie stream invertebrates consists
of the Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are characterized
by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and Ishnura, the
crustaceans (Hyalella and Gammarus), many genera and species of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Only 50% of the indicator species were present in this
sample for a D005 stream type indicating slight impairment. The Montana MMI ranks the community as
slightly impaired as well.

Macroinvertebrate Community Quality: MT MMI= 30.5 0/E= 50

Site Description

Jones Creek (site #1)

Figure 53. Jones Creek #1 (AES D005)
small remaining pool in reach

Figure 54. Jones Creek #1 (AES D005) dead snapping
turtle found on side ofRte. 85 bridge

Location: Accessed from Rt 85 at bridge crossing and proceeded upstream -25m to the first pool
designated the bottom of the reach.

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Typical Northern Great Plains Steppe

Aquatic Ecological System Type: D005-Northwestern Great Plains Intermittent Stream trending
toward E005 with a loss of connectivity to downstream fish colonization

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
moderate impacts

Rare or Unique Species: Snapping turtle was found dead on road near bridge (Figure 54).

Rare Features: No rare features documented

Introduced/Exotic Species: None

Overall Ecological Site Condition: Fair

Reach Summary: The 50 m reach consisted of 1 run/pool complex with the lower pool being -15m long
and produced by an earthen uprising (probably old cattle hummocking) and containing the only fish holding
habitat except for an artificially produced bridge pool not in the reach. This stream reach has sparse
aquatic habitat and low species diversity (1 fish species). The first run/pool complex proceeding

upstream was barely deep enough to allow seining for fish (Figure 53), but fathead minnows were
captured. All substrate of the pools was silt dominated with some embedded gravel in the run upstream.
The surrounding vegetation was dominated by Scirpus sp. (rushes) and Eleocharis palustris, common
spikerush. Aquatic vegetation and overhanging banks provided the most significant stream habitat in this
stream reach. Livestock use index (LUI) was moderate with -25 cow pies counted on a 50 m walk of
the left & right banks. Pugging and hummocking was especially noticeable below the lower pool area
where the cows have a stream crossing.

Reach Riparian Ranking: BLM= 66.7% (16 of 24) EPA RBP= 64% (125 of 200)

Amphibian Community: 1 adult Northern Leopard Frog (NLF) present. Undetermined toad, Bufo sp.,
tadpoles also present in pool.

Fish Community: 1 fish species (fathead minnow) was seined in the pool, none in the run. Expected
fish for this stream type (D005 trending toward E005) have been met.

Fish Community Quality: IBI= 44.77 0/E= 1/1.4 or 71%) of the expected reference fish.

Macroinvertebrate Community: This community of intermittent prairie stream invertebrates consists
of the Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are characterized
by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and Ishnura, the
crustaceans (Hyalella and Gammarus), many genera and species of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Over 60% of the indicator species were present in this
sample for a D005 stream type indicating slight impairment. The Montana MMI ranks the community as
slightly impaired as well.

Macroinvertebrate Community Quality: MT MMI= 35.6 0/E= 61.5

Intermittent Fishless Prairie Stream Ecological Type

Intermittent Fishless Prairie Stream (AES code E005). 1) Pine Spring Creek

Site Description

Pine Spring Creek (tributary to the South Fork Grand)

Figure 55. Pine Spring Creek (AES
E005) a Great Plains Fishless
Intermittent Stream with moderate
landscape integrity and degraded
local conditions

Location: Accessed from dirt road south of Rt 20, 1.2 miles east of Jump-Off Divide. Site was located
in a state-owned section at the culvert road-crossing then proceeded downstream -50m to the first bend
area.

Nearest Town: Buffalo, Harding County, SD

Ecoregion: Typical Northern Great Plains Steppe

Aquatic Ecological System Type: E005-Northwestern Great Plains Fishless Intermittent Stream

Key Environmental Factors: Hydrology — upstream dams or diversions in the watershed; Grazing —
moderate to severe impacts

Rare or Unique Species: No rare features documented

Rare Features: No rare features documented

Introduced/Exotic Species: None

Overall Ecological Site Condition: Poor/Fair

Reach Summary: The 100 m reach consisted of 1 run/pool complex with the run having been recently
refilled and the pool (-15m long) containing no fish and the only macro invertebrates in the reach. This
stream reach has sparse aquatic habitat and severely trampled riparian area. All substrate of the run was
silt dominated with some embedded gravel in the run upstream. The surrounding vegetation was
dominated by Carex nebrascensis (a heavy-grazing indicator), Scirpus sp. (rushes) and Eleocharis
palustris, common spikerush. Riparian vegetation and grassy banks were heavily grazed. Livestock use
index (LUI) was high -45 cow pies counted on a 50 m walk of the left & right banks. Pugging and
hummocking was especially noticeable at the top of the run where the cows have a stream crossing. This
sediment

Reach Habitat Ranking: BLM= 66.7% (16 of 24) EPA RBP= 63% (126 of 200)

Reach Riparian Geomorphology: The geomorphology of this stream reach is a Rosgen F-6 with a
gentle slope (-1%)), moderate sinuosity, a riffle-pool configuration with silt-dominated runs and pools.
Pools are slightly incised and averaged -25 cm in depth, wetted width of the reach averaged Im.
Surrounding bank materials are coarser than the channel bed materials indicating an accumulation of
sediments in the reach.

Amphibian Community: No amphibians reported from this site.

Fish Community: None

Macroinvertebrate Community: This community of intermittent prairie stream invertebrates consists
of the Prairie Pool assemblage (#12, Stagliano 2005). The community indicator species are characterized
by tolerant, damselfly taxa, Coenagrion/Enallagma sp. Enallagma civile, Lestes and Ishnura, the
crustaceans (Hyalella and Gammarus), many genera and species of the water boatman (Corixidae:
Sigara alternate, Trichocorixa nais, and Corisella), the snails (Physella, Gyraulus, and Stagnicola),
mayflies (Caenis and Callibaetis), and beetles (Oreodytes, Laccophilus, Hydroporus and Hygrotus).
As the complexity of the pool habitat decreases the dinger habitat species are lost, such as the
damselflies and many of the water boatman taxa. Over 60%) of the indicator species were present in this
sample for a E005 stream type indicating slight impairment. The Montana MMI ranks the community as
slightly impaired as well.

Macroinvertebrate Community Quality: MT MMI= 32.5 0/E= 61%

Conclusions

Diverse fish and macro invertebrate communities
were identified at many aquatic sites of the Slim
Buttes region, but the overall highest integrity sites
were in the South Fork Grand River basin. Most
stream sites visited in the Grand River basin had
higher than average landscape integrity reflected at
the local reach-scale with high biological integrity.
At this scale conservation work in the South Fork
Grand basin seems a logical choice, with excellent
restoration potential of the Jones Creek site
upstream from South Fork Grand #1. With the
exception of North Fork Moreau #2, the Moreau
basin sites exhibited less habitat integrity, more
disturbance and subsequently lower ranking fish
and macroinvertebrate communities. For a
Medium-Large Prairie River, the Little Missouri
River exhibits high quality fish and
macroinvertebrate communities. Diverse
communities with high biological integrity are highly
correlated with good riparian condition and high
habitat quality. Thus, effective riparian zone
management in the grazing of cattle will contribute
to intact vegetation buffers and less sediment in the
aquatic environment. Macroinvertebrate
communities ranked fewer sites as moderately
impaired, but the effectiveness of
macroinvertebrates in assessing prairie streams is
still under debate in Montana and has not been
addressed in South Dakota yet.

Community results from the habitat, fish and
macroinvertebrate surveys combined to rank the
following sites from highest biological integrity to
lowest within their aquatic ecological classification
codes:

Medium Prairie River (AES BOOS): 1) Little
Missouri Montana site, 2) Little Missouri #2, 3)
Little Missouri@ Camp Crook, 4) South Fork
Moreau #3

Northwestern Great Plains Prairie Stream

(AES COOS): 1) South Fork Grand #2, 2) South
Fork Grand #1,3) North Fork Moreau #2, 4) Jones
Creek #2, S) Crooked Creek, 6) South Fork
Moreau #2, 7) Bull Creek

Intermittent Prairie Stream (AES code DOOS):
1) North Fork Moreau #1,2) South Fork Moreau
#1; 3) Campbell Creek, 4) Spur Creek, S) Hay
Creek, 6) Jones Creek #1

Intermittent Fishless Prairie Stream (AES
code EOOS): 1) Pine Spring Creek

Northwestern Great Plains Perennial Spring

(AES code SOOS): 1) Picnic Spring

Jones Creek site #2, near the confluence with the
S. Fork Grand River, has high ecological potential
for recovery if hydrologic restoration occurs.

Literature Cited

Allan, J.D., D.L. Erickson and J. Fay. 1997. The
influence of catchment land use on stream
integrity across multiple spatial scales. Freshwa-
ter Biology 37:149-162.

Angermeier, P.L., and I.J. Schlosser. 1989. Spe-
cies-area relationships for stream fishes. Ecol-
ogy 70:1450-1462.

Barbour, M., J. Gerritsen, B.D. Snyder, and J.B.
Stribling. 1999. Rapid Bioassessment Protocols
for Use in Streams and Wadable Rivers: Per-
iphyton, Benthic Macroinvertebrates and Fish,
Second Edition. EPA841-B-99-002. United
States Environmental Protection Agency; Office
of Water: Washington, D.C.

Bramblett, R.G., and K.D. Fausch. 1991. Variable
fish communities and the index of biotic integrity
in a western Great Plains river. Transactions of
the American Fisheries Society 120:752-769.

Bramblett, R.G, TR. Johnson, A.V. Zale, A.V.,
andD. Heggem. 2005. Development and
Evaluation of a Fish Assemblage Index of Biotic
Integrity for Northwestern Great Plains. Trans-
actions of the American Fisheries Society
134:624-640.

Dodds, W.K., K. Gido, M.R. Whiles, K.M. Fritz,
and W.J. Matthews. 2004. Life on the edge:
The ecology of Great Plains prairie streams.
BioScience 54:205-216.

Feldman, D. 2006. Interpretation of New Macro-
invertebrate Models by WQPB. Draft
Report. Montana Department of Environmental
Quality, Planning Prevention and Assistance
Division, Water Quality Planning Bureau, Water
Quality Standards Section. 1520 E. 6^^ Avenue,
Helena, MT 59620. 14 pp.

Hawkins, C.P and R.H. Norris. 2000. Perfor-
mance of different landscape classifications for
aquatic bioassessments: Introduction to the
series. Journal of the North American
Benthological Society 19:3 (367-369).

Holton, G.D., and H.E. Johnson. 2003. Afield
guide to Montana fishes, 3rd edition. Montana
Fish, Wildlife and Parks, Helena.

Jessup, B. 2006. Ecological Data Application
System (EDAS), Version MT 3.3.2k. A User's
Guide. Tetra Tech, Inc.

Jessup, B., J. Stribling; and C. Hawkins. 2005.
Biological Indicators of Stream Condition in
Montana Using Macroinvertebrates. Tetra Tech,
Inc. November 2005 (draft).

Lazorchak, J.M., Klemm, D.J., and D.V. Peck
(editors). 1998. Environmental Monitoring and
Assessment Program - Surface Waters: Field
Operations and Methods for Measuring the
Ecological Condition of Wadeable Streams.
EPA/620/R-94/004F. U.S. Environmental
Protection Agency, Washington, D.C.

Loomis, TM. 1997. Survey of the fishes and
habitat in the Upper Moreau River, Perkins
County, South Dakota. South Dakota State
University, Brookings, SD. M.S. Thesis,
99pp+appendicies.

Matthews, W.J. and H.W. Robison. 1998. Influ-
ence of drainage connectivity, drainage area, and
regional species richness on fishes of the Interior
Highlands in Arkansas. American Midland
Naturalist 139:1-19.

Montana Department of Environmental Quality
(DEQ). 2005. Sample Collection, Sorting, and
Taxonomic Identification of Benthic Macroinver-
tebrates. Water Quality Planning Bureau.
Standard Operation Procedure (WQPBWQM-
009).

Montana Fish, Wildlife and Parks. 2003. Montana
Fish, Wildlife, and Parks Fish Sampling Protocols
for Prairie Streams. Written in Collaboration
with R.G. Bramblett, 2003. Helena, MT.

Omernik, J.M. 1995. Ecoregions: A Spatial
Framework for Environmental Management.
Chapter 5. Davis, W. and T. Simon, eds. Pages
49-64 in Biological Assessment and Criteria:
tools for water resource planning and decision
making. Lewis Publishers, Boca Raton, London.

Stagliano, David, M. 2005. Aquatic Community
Classification and Ecosystem Diversity in
Montana's Missouri River Watershed. Report to
the Bureau of Land Management. Montana
Natural Heritage Program, Helena, Montana. 65
pp. plus appendices, http://www.mtnhp.org/
reports. asp#Ecology

The Nature Conservancy. 1999. Seeing the forest
and the trees: Ecological Classification for
Conservation. The Nature Conservancy,
Arlington, Virginia. 25pp.

Werdon, S.J. 1992. Population status and charac-
teristics of Macrhybopsis gelida, Platygobio
gracilis and Rhinichthys cataractae in the
Missouri River Basin. South Dakota State
University, Brookings, SD. M.S. Thesis, 55pp.

Appendix A. Raw fish data and IBI metric calculations

COLLECTED FROM SlIM BuTTES SiTES. INTRODUCED SPECIES ARE

SHADED.

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Appendix A- 1

Appendix B. Macroinvertebrate taxa and abundance for the

Medium Prairie River sites

Taxa

Little Mo

Little

SF IVIoreau

iVlo#1

IVIo#2

Agabus

Acarina

Ablabesmyia

Ambrysus

Baetis intercalaris

Baetis tricaudatus

Caenis sp.

Caenis latipennis

Callibaetis

Centroptilum

Cercobrachys

Ceratopogoninae

Cheumatopsyche

147

Chironomus

Cladotanytarsus

Corixidae

Cricotopus

Cricotopus bicinctus

Cricotopus

(Isocladius)

Cryptochironomus

Cryptotendipes

Dicranota

Dicrotendipes

Dubiraphia

115

Dytiscidae

Enallagma

Ephoron

Fallceon quilleri

Gomphidae

Gomphus externus

Hyalella

Hydropsyche

Hydropsychidae

Hydroptila

Hygrobates

Isonychia

Ithytrichia

Labrundinia

Larsia

Leptophlebiidae

Leucrocuta

Mayatrichia

Microcylloepus

Nanocladius

Nectopsyche

Nematoda

Appendix

B-1

Taxa

Little IVIo

Littie

Little

SF IVIoreau

IV!o#1

IVIo #2

Neotrichia

Ochthebius

Oligochaeta

Ophiogomphus

severus

Ostracoda

Palmacorixa

Paracloeodes minutus

Paratanytarsus

Parakiefferiella

113

Physella

Polypedilum

Procladius

Pseudocloeon

Psectrocladius

Pseudochironomus

Rheotanytarsus

Saetheria tylus

Sialis

Sigara

Simulium

Sperchon

Stenelmis

Stenonema

Tanytarsus

Thienemanniella

Thienemannimyia

Tricorythodes

Tropisternus

Total Taxa Richness

Appendix B - 2

Appendix C. Significant indicator species (p<0.05) of the

MACROEWERTEBRATE COMMUNITY GROUPS. OIV=ObSERVED

Indicator Value of that taxon

Taxon

Group

OIV

Average

Std Dev

p-value

Transitional Prairie River

Cricotopus sp.

40.6

11.8

3.83

0.001

Rheotanytarsus

31.7

8.8

3.6

0.002

Tricorythodes

26.5

3.47

0.003

Cricotopus trifascia grp

31.5

7.9

3.79

0.003

Naididae

24.2

7.3

3.61

0.004

Oecetis avara grp

5.5

3.53

0.009

Monodiamesa sp.

14.1

4.8

3.04

0.015

Camelobatidius

15.5

5.3

3.16

0.015

Stenelmis sp.

21.4

7.8

4.3

0.016

Leucotrichia pictipes

13.9

4.6

2.91

0.017

Neotrichia sp.

13.9

3.19

0.022

Psychomyia sp.

11.2

4.7

2.93

0.039

Fallceon quilleri

13.7

6.8

3.34

0.041

Acentrella insignificans

7.1

3.62

0.043

Ephoron album

13.7

6.1

3.61

0.044

Travarella albertana

10.1

5.3

3.08

0.051

Prairie Stream Assemblage

Caenis latipennis

66.5

7.7

3.37

0.001

Ceratopogon sp.

37.1

8.5

3.94

0.001

Coenagrion

52.3

6.3

3.37

0.001

Labrundinia

26.2

3.9

2.51

0.001

Dubiraphia

21.1

3.8

2.48

0.002

Enallagma civile

17.6

3.8

2.35

0.003

Physella

27.7

11.1

3.52

0.005

Enallagma sp.

16.6

3.9

2.42

0.005

Sigara alternata

16.4

4.5

3.16

0.011

Psectrocladius

13.5

4.6

2.95

0.024

Sigara grosslineata

11.8

4.2

2.89

0.029

Trichocorixa

9.1

3.9

2.36

0.046

Large Prairie River Assemblage

Cheumatopsyche

54.7

9.9

3.18

0.001

Chironomidae

23.3

5.9

3.37

0.003

Neochoroterpes Oklahoma

16.6

4.2

2.7

0.005

Choroterpes

23.5

7.3

4.14

0.009

Ambrysus mormom

19.9

7.1

3.72

0.011

Hemerodromia

18.4

6.1

3.69

0.015

Microcylloepus

13.6

5.5

3.08

0.026

Hydropsyche morosa grp

12.2

5.8

3.16

0.044

Hydrochus

8.8

4.1

2.77

0.048

Prairie Stream Pool Assemblage

Hyalella

62.2

9.5

3.24

0.001

Coenagrion/Enallagma

32.7

4.8

2.67

0.001

Appendix C - 1

Taxon

Group

OIV

Average

Std Dev

p-value

Prairie Stream Pool Assemblage

Gammarus sp.

27.8

3.79

0.004

Callibaetis

30.4

7.4

4.02

0.005

Glyptotendipes

18.7

3.37

0.005

Trichocorixa nais

3.9

2.58

0.005

Gyraulus

22.4

7.2

3.79

0.008

Endochironomus

18.5

5.8

3.7

0.008

Haliplus

5.7

3.03

0.009

Paratanytarsus sp.

20.2

5.6

3.54

0.011

Mystacides sp.

13.2

4.2

2.76

0.015

Molanna

2.64

0.033

Hygrotus

9.8

4.1

2.72

0.044

Caenis youngi

9.1

4.1

2.63

0.049

Erpobdella

11.1

5.3

3.07

0.05

Corisella

9.4

4.2

2.87

0.05

Stagnicola

5.4

3.6

0.051

Collector-Filterer Assemblage

Simulium sp.

67.6

13.2

3.78

0.001

Isonychia sp.

21.4

6.6

3.87

0.01

Stylurus sp.

10.7

2.6

0.02

Eukiefferella claripennis grp

12.1

4.7

3.07

0.029

Pseudocloeon

9.4

4.4

2.85

0.049

Hydropsyche confusa

10.8

3.32

0.05

Medium River Side-Channel

Corixidae

71.1

8.4

3.26

0.001

Cryptotendipes

21.7

6.2

3.45

0.004

Placobdella

14.3

4.3

2.61

0.004

Tubifex

16.4

4.3

2.68

0.007

Procladius

20.4

6.9

3.31

0.008

Cryptochironomus

15.7

6.7

2.46

0.009

Stempelinella

18.8

5.5

3.36

0.013

Tanypus

14.5

6.2

3.54

0.041

Centroptilum

4.8

2.84

0.047

Gompus sp.

9.4

4.2

2.85

0.052

Palmacorixa gilletti

11.6

5.4

3.44

0.053

Probezzia

11.1

5.5

3.61

0.053

Appendix C - 2

Appendix D. Macroinvertebrate community descriptions
(SPA-SPECIES assemblage) (from Stagliano 2005).

Group 3 - Transitional Prairie River Assemblage. This widespread community type occurred in the
Little Missouri River (4^^ -T^ order medium to large warmwater rivers). The habitat quality of these
systems was rated medium to high with grazing and agriculture dominant land uses in these systems, so
sediment could be a problem. Genera associated with this group are moderately tolerant to sediment and
nutrients. Representative indicator taxa: Camelobatidius, Stenelmis, Leucotrichia pictipes,
Tricorythodes.

Group 9 - Prairie Stream Assemblage. This ubiquitous prairie stream community type is found in all
basins and is associated with small to medium (2nd-5th order) prairie streams with the lowest elevation
and gradient. Although this group is found in small to large stream systems, it typically occurs in slow
current areas with silted, sand /gravel /cobble substrates, often with aquatic vegetation. The riffle areas of
these may have clean mixed cobble substrates similar to Group 3 habitats, but with less flow. Prairie
streams examples: S F Grand River, Jones Creek #2. Indicator taxa are typical of low-gradient streams
and are tolerant to disturbance: Caenis latipennis, Ceratopogon, Coenagrion, Enallagma civile,
Physella, Dubiraphia.

Group 11 - Large Prairie River Assemblage. This group occurred in downstream confluence areas
and is associated with warm-water medium and large rivers (4^^-7^^ order) of lower elevation and
moderate gradient. Although this group is a large stream system community similar to Group 1 , it is found
in areas with more agricultural land use and sediment deposition than Group 1. Indicator taxa are
relatively tolerant to disturbance and typical of low gradient streams with stable substrates and a slow-
moderate current velocity. Example rivers: Frenchman Creek, Missouri River, and Powder Rivers.
Indicator taxa consist of genera from many insect orders tolerant of sedimentation and moderate pollution:
Cheumatopsyche, Neochoroterpes Oklahoma, Choroterpes, Ambrysus mormom, Hemerodromia,
Microcylloepus, Hydropsyche morosa grp.

Group 12 - Prairie Pool Assemblage. This group is associated with slow-moving small to medium
warm- water prairie streams {T"^ -5^^ order) of low-mid elevation, low gradient, typically with heavy
aquatic vegetation and low current or stagnant pool areas. Group 12 is a highly tolerant group of
invertebrates that can withstand low oxygen, high temperatures and siltation. Even though this group can
be found in large warmwater prairie systems, similar to Groups 9 and 1 1, it is found in areas with less
current and higher sediment influences. Stream examples: Hanging Woman, Sarpy, Coffee, O'Fallon
Creek, Thompson, Otter Creeks. Indicator taxa: Hyalella, Coenagrion/Enallagma, Gammarus sp.,
Callibaetis, Glyptotendipes, Trichocorixa nais, Gyraulus, Erpobdella, Corisella, Stagnicola

Group 37 - Filtering-Collector Assemblage. This moderately tolerant macro invertebrate group is
associated with warm- water medium and large rivers (4^^-6^^ order) of low elevation (2000-3500 ft), high
nutrient/turbidity and slow-moderate current velocity with stablea shifting substrates. This community
occurs in sand/gravel substrates of large rivers (A003, BOOS) or smaller (COOS) degraded streams with
sediment and nutrient problems. Two indicator taxa, Simulium and Hydropsyche confusa, can quickly
colonize newly exposed substrates, so shifting sediments will not disturb this community. Most indicator
taxa are filterer-collectors or predators and can tolerate streams with higher sediment influences than
most other large stream/ river communities. Stream and river examples: Little Missouri River, SF Grand,
NF Moreau. Indicator taxa: Simulium, Isonychia, Stylurus, Eukiefferella claripennis grp.,
Pseudocloeon, Hydropsyche confusa

Appendix D - 1

Group 40- Medium River Side-Channel Community. This community group consisting of
moderately tolerant macroinvertebrates is associated with medium to large (3^'^-6^^ order) warmwater
rivers, medium turbidity, moderate gradients, low elevation (2500-4000 ft.) gravel/cobble dominated with
silted side channels. Slim Butte River examples: Little Missouri, SF Moreau and Jones Creek #2.
Indicator taxa include: Corixidae, Cryptotendipes, Placobdella, Tubifex, Procladius,
Cryptochironomus, Stempelinella

Appendix D - 2

Appendix E. Fish community descriptions (SPA-species
assemblage) (from Stagliano 2005).

Group SPA #1-Large Warmwater River Assemblage. This community was dominated by larger,
warmwater river fishes, including many of our natives, such as the sauger (Stizostedium canadanse), big
(Ictiobus cyprinellus) and smallmouth buffalo (Ictiobus bubalus) and the emerald shiner (Notropis
atherinoides), but also included fish species introduced to the Missouri and Yellowstone drainages:
smallmouth bass (Micropterus dolomieu), perch {Perca flavescens), walleye {Stizostedium vitreum)
and northern pike {Esox lucius). Warmwater generalists such as sunfish, bass and golden shiners are
also closely associated with this group in the Yellowstone drainages. As a general rule this assemblage is
found in larger, low gradient, glide-pool main branch streams (4^^ -6^^ order) with an average summer
temperature of 20-25°C. The 2 native ictalurid species, the stonecat {Noturus flavus) and the channel
catfish (Jctalurus punctatus), also cluster in this assemblage. This community can be found over a wide
range of low-elevation landscapes within all three ecoregions of the study area.

Group SPA #2- Medium Warmwater River Assemblage. Most of the medium to large warmwater
river cyprinid species occur in this species assemblage (flathead chub, Platygobio gracilis', sand shiner,
Notropis stramineus; plains minnow, Hybognathus placitus; western silvery minnow, Hybognathus
argyritis), as well as the shorthead redhorse (Moxostoma macrolepidotum), river carpsucker
(Carpiodes carpio), the exotic carp (Cyprinus carpio), the introduced green sunfish (Lepomis
cyanellus) and black bullhead (Ameiurus melas). This species assemblage occurs in most of the
Medium Prairie Rivers of Montana. The channel catfish & stonecat could co-occur within SPA 1 or 2 if
proper habitat requirements are met, such as deep, side channel pools and large structures for hiding
(large cobbles and woody debris).

Group SPA #18-Brook Stickleback Assemblage. Includes the brook stickleback (Culaea
inconstans), brassy minnow {Hybognathus hankinsoni) and Iowa Darter (Etheostoma exile). This
species assemblage is found most commonly associated with small Northwestern Great Plains prairie
streams (AES C006 and D006) with relatively clear water, large pools and vegetative cover.

Group SPA # 20-Core Prairie Stream Assemblage. Includes an assemblage of small native prairie
fish that form the core community for perennial prairie streams (AES code COOS in the Northwestern
Great Plains and C006 in the Northern Glaciated ecoregions. Included in this assemblage are the
longnose dace (Rhinichthys cataractae), lake chub (Couesius plumbeus), fathead minnow (Pimephales
notatus) and the white sucker (Catostomus commersoni). The lake chub and fathead minnow
{Pimephales notatus) are species that occur in similar habitats of intermittent prairie stream systems
D005 and D006, although we found no lake chubs in any of the Slim Butte streams. As the small prairie
streams dominated by this core species assemblage proceed downstream and increase stream order and
linkages, they develop into the Medium Prairie River Community including the plains and western silvery
minnows (plains minnow is more tolerant of current, while the western silvery will be found in the
protected silted side channels out of the current), and the sand shiner (in slower pools of BOOS or larger
streams with gravelly /sandy bottoms), and the exotic carp and introduced black bullhead.

Appendix E - 1

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